diff --git a/build/gobind-pinecone/monolith.go b/build/gobind-pinecone/monolith.go
index 60e817212..44eab4cd7 100644
--- a/build/gobind-pinecone/monolith.go
+++ b/build/gobind-pinecone/monolith.go
@@ -243,7 +243,10 @@ func (m *DendriteMonolith) Start() {
 
 	prefix := hex.EncodeToString(pk)
 	cfg := &config.Dendrite{}
-	cfg.Defaults(true)
+	cfg.Defaults(config.DefaultOpts{
+		Generate:   true,
+		Monolithic: true,
+	})
 	cfg.Global.ServerName = gomatrixserverlib.ServerName(hex.EncodeToString(pk))
 	cfg.Global.PrivateKey = sk
 	cfg.Global.KeyID = gomatrixserverlib.KeyID(signing.KeyID)
diff --git a/build/gobind-yggdrasil/monolith.go b/build/gobind-yggdrasil/monolith.go
index 4432a3a45..896f3d14f 100644
--- a/build/gobind-yggdrasil/monolith.go
+++ b/build/gobind-yggdrasil/monolith.go
@@ -82,7 +82,10 @@ func (m *DendriteMonolith) Start() {
 	m.YggdrasilNode = ygg
 
 	cfg := &config.Dendrite{}
-	cfg.Defaults(true)
+	cfg.Defaults(config.DefaultOpts{
+		Generate:   true,
+		Monolithic: true,
+	})
 	cfg.Global.ServerName = gomatrixserverlib.ServerName(ygg.DerivedServerName())
 	cfg.Global.PrivateKey = ygg.PrivateKey()
 	cfg.Global.KeyID = gomatrixserverlib.KeyID(signing.KeyID)
diff --git a/build/scripts/ComplementPostgres.Dockerfile b/build/scripts/ComplementPostgres.Dockerfile
index 699540120..785090b0b 100644
--- a/build/scripts/ComplementPostgres.Dockerfile
+++ b/build/scripts/ComplementPostgres.Dockerfile
@@ -46,9 +46,8 @@ EXPOSE 8008 8448
 # At runtime, generate TLS cert based on the CA now mounted at /ca
 # At runtime, replace the SERVER_NAME with what we are told
 CMD /build/run_postgres.sh && ./generate-keys --keysize 1024 --server $SERVER_NAME --tls-cert server.crt --tls-key server.key --tls-authority-cert /complement/ca/ca.crt --tls-authority-key /complement/ca/ca.key && \
-    ./generate-config -server $SERVER_NAME --ci > dendrite.yaml && \
-    # Replace the connection string with a single postgres DB, using user/db = 'postgres' and no password, bump max_conns
-    sed -i "s%connection_string:.*$%connection_string: postgresql://postgres@localhost/postgres?sslmode=disable%g" dendrite.yaml && \
-    sed -i 's/max_open_conns:.*$/max_open_conns: 100/g' dendrite.yaml && \
+    ./generate-config -server $SERVER_NAME --ci --db postgresql://postgres@localhost/postgres?sslmode=disable > dendrite.yaml && \
+    # Bump max_open_conns up here in the global database config
+    sed -i 's/max_open_conns:.*$/max_open_conns: 1990/g' dendrite.yaml && \
     cp /complement/ca/ca.crt /usr/local/share/ca-certificates/ && update-ca-certificates && \
     exec ./dendrite-monolith-server --really-enable-open-registration --tls-cert server.crt --tls-key server.key --config dendrite.yaml -api=${API:-0}
\ No newline at end of file
diff --git a/clientapi/routing/register_test.go b/clientapi/routing/register_test.go
index 0507116f1..85846c7d6 100644
--- a/clientapi/routing/register_test.go
+++ b/clientapi/routing/register_test.go
@@ -181,7 +181,10 @@ func TestValidationOfApplicationServices(t *testing.T) {
 
 	// Set up a config
 	fakeConfig := &config.Dendrite{}
-	fakeConfig.Defaults(true)
+	fakeConfig.Defaults(config.DefaultOpts{
+		Generate:   true,
+		Monolithic: true,
+	})
 	fakeConfig.Global.ServerName = "localhost"
 	fakeConfig.ClientAPI.Derived.ApplicationServices = []config.ApplicationService{fakeApplicationService}
 
diff --git a/cmd/dendrite-demo-pinecone/main.go b/cmd/dendrite-demo-pinecone/main.go
index 52c9dc8eb..83b52132a 100644
--- a/cmd/dendrite-demo-pinecone/main.go
+++ b/cmd/dendrite-demo-pinecone/main.go
@@ -115,7 +115,10 @@ func main() {
 				panic("failed to load PEM key: " + err.Error())
 			}
 		}
-		cfg.Defaults(true)
+		cfg.Defaults(config.DefaultOpts{
+			Generate:   true,
+			Monolithic: true,
+		})
 		cfg.Global.PrivateKey = sk
 		cfg.Global.JetStream.StoragePath = config.Path(fmt.Sprintf("%s/", *instanceName))
 		cfg.UserAPI.AccountDatabase.ConnectionString = config.DataSource(fmt.Sprintf("file:%s-account.db", *instanceName))
diff --git a/cmd/dendrite-demo-yggdrasil/main.go b/cmd/dendrite-demo-yggdrasil/main.go
index 086baa264..d2fddf8bc 100644
--- a/cmd/dendrite-demo-yggdrasil/main.go
+++ b/cmd/dendrite-demo-yggdrasil/main.go
@@ -78,7 +78,10 @@ func main() {
 	if configFlagSet {
 		cfg = setup.ParseFlags(true)
 	} else {
-		cfg.Defaults(true)
+		cfg.Defaults(config.DefaultOpts{
+			Generate:   true,
+			Monolithic: true,
+		})
 		cfg.Global.JetStream.StoragePath = config.Path(fmt.Sprintf("%s/", *instanceName))
 		cfg.UserAPI.AccountDatabase.ConnectionString = config.DataSource(fmt.Sprintf("file:%s-account.db", *instanceName))
 		cfg.MediaAPI.Database.ConnectionString = config.DataSource(fmt.Sprintf("file:%s-mediaapi.db", *instanceName))
diff --git a/cmd/generate-config/main.go b/cmd/generate-config/main.go
index 6ae3ff9c9..c24e8153e 100644
--- a/cmd/generate-config/main.go
+++ b/cmd/generate-config/main.go
@@ -3,6 +3,7 @@ package main
 import (
 	"flag"
 	"fmt"
+	"path/filepath"
 
 	"github.com/matrix-org/dendrite/setup/config"
 	"github.com/matrix-org/gomatrixserverlib"
@@ -11,90 +12,81 @@ import (
 )
 
 func main() {
-	defaultsForCI := flag.Bool("ci", false, "sane defaults for CI testing")
+	defaultsForCI := flag.Bool("ci", false, "Populate the configuration with sane defaults for use in CI")
 	serverName := flag.String("server", "", "The domain name of the server if not 'localhost'")
-	dbURI := flag.String("db", "", "The DB URI to use for all components if not SQLite files")
+	dbURI := flag.String("db", "", "The DB URI to use for all components (PostgreSQL only)")
+	dirPath := flag.String("dir", "./", "The folder to use for paths (like SQLite databases, media storage)")
+	normalise := flag.String("normalise", "", "Normalise an existing configuration file by adding new/missing options and defaults")
+	polylith := flag.Bool("polylith", false, "Generate a config that makes sense for polylith deployments")
 	flag.Parse()
 
-	cfg := &config.Dendrite{
-		Version: config.Version,
-	}
-	cfg.Defaults(true)
-	if *serverName != "" {
-		cfg.Global.ServerName = gomatrixserverlib.ServerName(*serverName)
-	}
-	if *dbURI != "" {
-		cfg.FederationAPI.Database.ConnectionString = config.DataSource(*dbURI)
-		cfg.KeyServer.Database.ConnectionString = config.DataSource(*dbURI)
-		cfg.MSCs.Database.ConnectionString = config.DataSource(*dbURI)
-		cfg.MediaAPI.Database.ConnectionString = config.DataSource(*dbURI)
-		cfg.RoomServer.Database.ConnectionString = config.DataSource(*dbURI)
-		cfg.SyncAPI.Database.ConnectionString = config.DataSource(*dbURI)
-		cfg.UserAPI.AccountDatabase.ConnectionString = config.DataSource(*dbURI)
-	}
-	cfg.Global.TrustedIDServers = []string{
-		"matrix.org",
-		"vector.im",
-	}
-	cfg.Logging = []config.LogrusHook{
-		{
-			Type:  "file",
-			Level: "info",
-			Params: map[string]interface{}{
-				"path": "/var/log/dendrite",
-			},
-		},
-	}
-	cfg.FederationAPI.KeyPerspectives = config.KeyPerspectives{
-		{
-			ServerName: "matrix.org",
-			Keys: []config.KeyPerspectiveTrustKey{
-				{
-					KeyID:     "ed25519:auto",
-					PublicKey: "Noi6WqcDj0QmPxCNQqgezwTlBKrfqehY1u2FyWP9uYw",
-				},
-				{
-					KeyID:     "ed25519:a_RXGa",
-					PublicKey: "l8Hft5qXKn1vfHrg3p4+W8gELQVo8N13JkluMfmn2sQ",
+	var cfg *config.Dendrite
+	if *normalise == "" {
+		cfg = &config.Dendrite{
+			Version: config.Version,
+		}
+		cfg.Defaults(config.DefaultOpts{
+			Generate:   true,
+			Monolithic: !*polylith,
+		})
+		if *serverName != "" {
+			cfg.Global.ServerName = gomatrixserverlib.ServerName(*serverName)
+		}
+		uri := config.DataSource(*dbURI)
+		if *polylith || uri.IsSQLite() || uri == "" {
+			for name, db := range map[string]*config.DatabaseOptions{
+				"federationapi": &cfg.FederationAPI.Database,
+				"keyserver":     &cfg.KeyServer.Database,
+				"mscs":          &cfg.MSCs.Database,
+				"mediaapi":      &cfg.MediaAPI.Database,
+				"roomserver":    &cfg.RoomServer.Database,
+				"syncapi":       &cfg.SyncAPI.Database,
+				"userapi":       &cfg.UserAPI.AccountDatabase,
+			} {
+				if uri == "" {
+					path := filepath.Join(*dirPath, fmt.Sprintf("dendrite_%s.db", name))
+					db.ConnectionString = config.DataSource(fmt.Sprintf("file:%s", path))
+				} else {
+					db.ConnectionString = uri
+				}
+			}
+		} else {
+			cfg.Global.DatabaseOptions.ConnectionString = uri
+		}
+		cfg.Logging = []config.LogrusHook{
+			{
+				Type:  "file",
+				Level: "info",
+				Params: map[string]interface{}{
+					"path": filepath.Join(*dirPath, "log"),
 				},
 			},
-		},
-	}
-	cfg.MediaAPI.ThumbnailSizes = []config.ThumbnailSize{
-		{
-			Width:        32,
-			Height:       32,
-			ResizeMethod: "crop",
-		},
-		{
-			Width:        96,
-			Height:       96,
-			ResizeMethod: "crop",
-		},
-		{
-			Width:        640,
-			Height:       480,
-			ResizeMethod: "scale",
-		},
-	}
-
-	if *defaultsForCI {
-		cfg.AppServiceAPI.DisableTLSValidation = true
-		cfg.ClientAPI.RateLimiting.Enabled = false
-		cfg.FederationAPI.DisableTLSValidation = false
-		// don't hit matrix.org when running tests!!!
-		cfg.FederationAPI.KeyPerspectives = config.KeyPerspectives{}
-		cfg.MSCs.MSCs = []string{"msc2836", "msc2946", "msc2444", "msc2753"}
-		cfg.Logging[0].Level = "trace"
-		cfg.Logging[0].Type = "std"
-		cfg.UserAPI.BCryptCost = bcrypt.MinCost
-		cfg.Global.JetStream.InMemory = true
-		cfg.ClientAPI.RegistrationDisabled = false
-		cfg.ClientAPI.OpenRegistrationWithoutVerificationEnabled = true
-		cfg.ClientAPI.RegistrationSharedSecret = "complement"
-		cfg.Global.Presence = config.PresenceOptions{
-			EnableInbound:  true,
-			EnableOutbound: true,
+		}
+		if *defaultsForCI {
+			cfg.AppServiceAPI.DisableTLSValidation = true
+			cfg.ClientAPI.RateLimiting.Enabled = false
+			cfg.FederationAPI.DisableTLSValidation = false
+			// don't hit matrix.org when running tests!!!
+			cfg.FederationAPI.KeyPerspectives = config.KeyPerspectives{}
+			cfg.MediaAPI.BasePath = config.Path(filepath.Join(*dirPath, "media"))
+			cfg.MSCs.MSCs = []string{"msc2836", "msc2946", "msc2444", "msc2753"}
+			cfg.Logging[0].Level = "trace"
+			cfg.Logging[0].Type = "std"
+			cfg.UserAPI.BCryptCost = bcrypt.MinCost
+			cfg.Global.JetStream.InMemory = true
+			cfg.Global.JetStream.StoragePath = config.Path(*dirPath)
+			cfg.ClientAPI.RegistrationDisabled = false
+			cfg.ClientAPI.OpenRegistrationWithoutVerificationEnabled = true
+			cfg.ClientAPI.RegistrationSharedSecret = "complement"
+			cfg.Global.Presence = config.PresenceOptions{
+				EnableInbound:  true,
+				EnableOutbound: true,
+			}
+		}
+	} else {
+		var err error
+		if cfg, err = config.Load(*normalise, !*polylith); err != nil {
+			panic(err)
 		}
 	}
 
diff --git a/federationapi/federationapi_keys_test.go b/federationapi/federationapi_keys_test.go
index 9c3446222..4469da35b 100644
--- a/federationapi/federationapi_keys_test.go
+++ b/federationapi/federationapi_keys_test.go
@@ -75,7 +75,10 @@ func TestMain(m *testing.M) {
 			// Draw up just enough Dendrite config for the server key
 			// API to work.
 			cfg := &config.Dendrite{}
-			cfg.Defaults(true)
+			cfg.Defaults(config.DefaultOpts{
+				Generate:   true,
+				Monolithic: true,
+			})
 			cfg.Global.ServerName = gomatrixserverlib.ServerName(s.name)
 			cfg.Global.PrivateKey = testPriv
 			cfg.Global.JetStream.InMemory = true
diff --git a/federationapi/federationapi_test.go b/federationapi/federationapi_test.go
index bdcb9f57c..15f7a6840 100644
--- a/federationapi/federationapi_test.go
+++ b/federationapi/federationapi_test.go
@@ -263,7 +263,10 @@ func testFederationAPIJoinThenKeyUpdate(t *testing.T, dbType test.DBType) {
 func TestRoomsV3URLEscapeDoNot404(t *testing.T) {
 	_, privKey, _ := ed25519.GenerateKey(nil)
 	cfg := &config.Dendrite{}
-	cfg.Defaults(true)
+	cfg.Defaults(config.DefaultOpts{
+		Generate:   true,
+		Monolithic: true,
+	})
 	cfg.Global.KeyID = gomatrixserverlib.KeyID("ed25519:auto")
 	cfg.Global.ServerName = gomatrixserverlib.ServerName("localhost")
 	cfg.Global.PrivateKey = privKey
diff --git a/setup/config/config.go b/setup/config/config.go
index cc9c04470..5a618d671 100644
--- a/setup/config/config.go
+++ b/setup/config/config.go
@@ -211,7 +211,10 @@ func loadConfig(
 	monolithic bool,
 ) (*Dendrite, error) {
 	var c Dendrite
-	c.Defaults(false)
+	c.Defaults(DefaultOpts{
+		Generate:   false,
+		Monolithic: monolithic,
+	})
 	c.IsMonolith = monolithic
 
 	var err error
@@ -295,21 +298,25 @@ func (config *Dendrite) Derive() error {
 	return nil
 }
 
+type DefaultOpts struct {
+	Generate   bool
+	Monolithic bool
+}
+
 // SetDefaults sets default config values if they are not explicitly set.
-func (c *Dendrite) Defaults(generate bool) {
+func (c *Dendrite) Defaults(opts DefaultOpts) {
 	c.Version = Version
 
-	c.Global.Defaults(generate)
-	c.ClientAPI.Defaults(generate)
-	c.FederationAPI.Defaults(generate)
-	c.KeyServer.Defaults(generate)
-	c.MediaAPI.Defaults(generate)
-	c.RoomServer.Defaults(generate)
-	c.SyncAPI.Defaults(generate)
-	c.UserAPI.Defaults(generate)
-	c.AppServiceAPI.Defaults(generate)
-	c.MSCs.Defaults(generate)
-
+	c.Global.Defaults(opts)
+	c.ClientAPI.Defaults(opts)
+	c.FederationAPI.Defaults(opts)
+	c.KeyServer.Defaults(opts)
+	c.MediaAPI.Defaults(opts)
+	c.RoomServer.Defaults(opts)
+	c.SyncAPI.Defaults(opts)
+	c.UserAPI.Defaults(opts)
+	c.AppServiceAPI.Defaults(opts)
+	c.MSCs.Defaults(opts)
 	c.Wiring()
 }
 
diff --git a/setup/config/config_appservice.go b/setup/config/config_appservice.go
index 9c3771272..bd21826fe 100644
--- a/setup/config/config_appservice.go
+++ b/setup/config/config_appservice.go
@@ -29,7 +29,7 @@ type AppServiceAPI struct {
 	Matrix  *Global  `yaml:"-"`
 	Derived *Derived `yaml:"-"` // TODO: Nuke Derived from orbit
 
-	InternalAPI InternalAPIOptions `yaml:"internal_api"`
+	InternalAPI InternalAPIOptions `yaml:"internal_api,omitempty"`
 
 	// DisableTLSValidation disables the validation of X.509 TLS certs
 	// on appservice endpoints. This is not recommended in production!
@@ -38,9 +38,11 @@ type AppServiceAPI struct {
 	ConfigFiles []string `yaml:"config_files"`
 }
 
-func (c *AppServiceAPI) Defaults(generate bool) {
-	c.InternalAPI.Listen = "http://localhost:7777"
-	c.InternalAPI.Connect = "http://localhost:7777"
+func (c *AppServiceAPI) Defaults(opts DefaultOpts) {
+	if !opts.Monolithic {
+		c.InternalAPI.Listen = "http://localhost:7777"
+		c.InternalAPI.Connect = "http://localhost:7777"
+	}
 }
 
 func (c *AppServiceAPI) Verify(configErrs *ConfigErrors, isMonolith bool) {
diff --git a/setup/config/config_clientapi.go b/setup/config/config_clientapi.go
index ecf8f6bd5..56f4b3f92 100644
--- a/setup/config/config_clientapi.go
+++ b/setup/config/config_clientapi.go
@@ -9,8 +9,8 @@ type ClientAPI struct {
 	Matrix  *Global  `yaml:"-"`
 	Derived *Derived `yaml:"-"` // TODO: Nuke Derived from orbit
 
-	InternalAPI InternalAPIOptions `yaml:"internal_api"`
-	ExternalAPI ExternalAPIOptions `yaml:"external_api"`
+	InternalAPI InternalAPIOptions `yaml:"internal_api,omitempty"`
+	ExternalAPI ExternalAPIOptions `yaml:"external_api,omitempty"`
 
 	// If set disables new users from registering (except via shared
 	// secrets)
@@ -48,13 +48,15 @@ type ClientAPI struct {
 	// Rate-limiting options
 	RateLimiting RateLimiting `yaml:"rate_limiting"`
 
-	MSCs *MSCs `yaml:"mscs"`
+	MSCs *MSCs `yaml:"-"`
 }
 
-func (c *ClientAPI) Defaults(generate bool) {
-	c.InternalAPI.Listen = "http://localhost:7771"
-	c.InternalAPI.Connect = "http://localhost:7771"
-	c.ExternalAPI.Listen = "http://[::]:8071"
+func (c *ClientAPI) Defaults(opts DefaultOpts) {
+	if !opts.Monolithic {
+		c.InternalAPI.Listen = "http://localhost:7771"
+		c.InternalAPI.Connect = "http://localhost:7771"
+		c.ExternalAPI.Listen = "http://[::]:8071"
+	}
 	c.RegistrationSharedSecret = ""
 	c.RecaptchaPublicKey = ""
 	c.RecaptchaPrivateKey = ""
diff --git a/setup/config/config_federationapi.go b/setup/config/config_federationapi.go
index a7a515fda..d3a4b2b67 100644
--- a/setup/config/config_federationapi.go
+++ b/setup/config/config_federationapi.go
@@ -5,12 +5,12 @@ import "github.com/matrix-org/gomatrixserverlib"
 type FederationAPI struct {
 	Matrix *Global `yaml:"-"`
 
-	InternalAPI InternalAPIOptions `yaml:"internal_api"`
-	ExternalAPI ExternalAPIOptions `yaml:"external_api"`
+	InternalAPI InternalAPIOptions `yaml:"internal_api,omitempty"`
+	ExternalAPI ExternalAPIOptions `yaml:"external_api,omitempty"`
 
 	// The database stores information used by the federation destination queues to
 	// send transactions to remote servers.
-	Database DatabaseOptions `yaml:"database"`
+	Database DatabaseOptions `yaml:"database,omitempty"`
 
 	// Federation failure threshold. How many consecutive failures that we should
 	// tolerate when sending federation requests to a specific server. The backoff
@@ -30,25 +30,44 @@ type FederationAPI struct {
 	PreferDirectFetch bool `yaml:"prefer_direct_fetch"`
 }
 
-func (c *FederationAPI) Defaults(generate bool) {
-	c.InternalAPI.Listen = "http://localhost:7772"
-	c.InternalAPI.Connect = "http://localhost:7772"
-	c.ExternalAPI.Listen = "http://[::]:8072"
+func (c *FederationAPI) Defaults(opts DefaultOpts) {
+	if !opts.Monolithic {
+		c.InternalAPI.Listen = "http://localhost:7772"
+		c.InternalAPI.Connect = "http://localhost:7772"
+		c.ExternalAPI.Listen = "http://[::]:8072"
+		c.Database.Defaults(10)
+	}
 	c.FederationMaxRetries = 16
 	c.DisableTLSValidation = false
-	c.Database.Defaults(10)
-	if generate {
-		c.Database.ConnectionString = "file:federationapi.db"
+	if opts.Generate {
+		c.KeyPerspectives = KeyPerspectives{
+			{
+				ServerName: "matrix.org",
+				Keys: []KeyPerspectiveTrustKey{
+					{
+						KeyID:     "ed25519:auto",
+						PublicKey: "Noi6WqcDj0QmPxCNQqgezwTlBKrfqehY1u2FyWP9uYw",
+					},
+					{
+						KeyID:     "ed25519:a_RXGa",
+						PublicKey: "l8Hft5qXKn1vfHrg3p4+W8gELQVo8N13JkluMfmn2sQ",
+					},
+				},
+			},
+		}
+		if !opts.Monolithic {
+			c.Database.ConnectionString = "file:federationapi.db"
+		}
 	}
 }
 
 func (c *FederationAPI) Verify(configErrs *ConfigErrors, isMonolith bool) {
-	if c.Matrix.DatabaseOptions.ConnectionString == "" {
-		checkNotEmpty(configErrs, "federation_api.database.connection_string", string(c.Database.ConnectionString))
-	}
 	if isMonolith { // polylith required configs below
 		return
 	}
+	if c.Matrix.DatabaseOptions.ConnectionString == "" {
+		checkNotEmpty(configErrs, "federation_api.database.connection_string", string(c.Database.ConnectionString))
+	}
 	checkURL(configErrs, "federation_api.external_api.listen", string(c.ExternalAPI.Listen))
 	checkURL(configErrs, "federation_api.internal_api.listen", string(c.InternalAPI.Listen))
 	checkURL(configErrs, "federation_api.internal_api.connect", string(c.InternalAPI.Connect))
diff --git a/setup/config/config_global.go b/setup/config/config_global.go
index d4e54e203..acc608dd7 100644
--- a/setup/config/config_global.go
+++ b/setup/config/config_global.go
@@ -41,7 +41,7 @@ type Global struct {
 	// connections will be used instead. This way we don't have to manage connection
 	// counts on a per-component basis, but can instead do it for the entire monolith.
 	// In a polylith deployment, this will be ignored.
-	DatabaseOptions DatabaseOptions `yaml:"database"`
+	DatabaseOptions DatabaseOptions `yaml:"database,omitempty"`
 
 	// The server name to delegate server-server communications to, with optional port
 	WellKnownServerName string `yaml:"well_known_server_name"`
@@ -83,22 +83,28 @@ type Global struct {
 	Cache Cache `yaml:"cache"`
 }
 
-func (c *Global) Defaults(generate bool) {
-	if generate {
+func (c *Global) Defaults(opts DefaultOpts) {
+	if opts.Generate {
 		c.ServerName = "localhost"
 		c.PrivateKeyPath = "matrix_key.pem"
 		_, c.PrivateKey, _ = ed25519.GenerateKey(rand.New(rand.NewSource(0)))
 		c.KeyID = "ed25519:auto"
+		c.TrustedIDServers = []string{
+			"matrix.org",
+			"vector.im",
+		}
 	}
 	c.KeyValidityPeriod = time.Hour * 24 * 7
-
-	c.JetStream.Defaults(generate)
-	c.Metrics.Defaults(generate)
+	if opts.Monolithic {
+		c.DatabaseOptions.Defaults(90)
+	}
+	c.JetStream.Defaults(opts)
+	c.Metrics.Defaults(opts)
 	c.DNSCache.Defaults()
 	c.Sentry.Defaults()
-	c.ServerNotices.Defaults(generate)
+	c.ServerNotices.Defaults(opts)
 	c.ReportStats.Defaults()
-	c.Cache.Defaults(generate)
+	c.Cache.Defaults()
 }
 
 func (c *Global) Verify(configErrs *ConfigErrors, isMonolith bool) {
@@ -142,9 +148,9 @@ type Metrics struct {
 	} `yaml:"basic_auth"`
 }
 
-func (c *Metrics) Defaults(generate bool) {
+func (c *Metrics) Defaults(opts DefaultOpts) {
 	c.Enabled = false
-	if generate {
+	if opts.Generate {
 		c.BasicAuth.Username = "metrics"
 		c.BasicAuth.Password = "metrics"
 	}
@@ -166,8 +172,8 @@ type ServerNotices struct {
 	RoomName string `yaml:"room_name"`
 }
 
-func (c *ServerNotices) Defaults(generate bool) {
-	if generate {
+func (c *ServerNotices) Defaults(opts DefaultOpts) {
+	if opts.Generate {
 		c.Enabled = true
 		c.LocalPart = "_server"
 		c.DisplayName = "Server Alert"
@@ -183,7 +189,7 @@ type Cache struct {
 	MaxAge           time.Duration `yaml:"max_age"`
 }
 
-func (c *Cache) Defaults(generate bool) {
+func (c *Cache) Defaults() {
 	c.EstimatedMaxSize = 1024 * 1024 * 1024 // 1GB
 	c.MaxAge = time.Hour
 }
diff --git a/setup/config/config_jetstream.go b/setup/config/config_jetstream.go
index a7827597e..ef8bf014b 100644
--- a/setup/config/config_jetstream.go
+++ b/setup/config/config_jetstream.go
@@ -31,10 +31,10 @@ func (c *JetStream) Durable(name string) string {
 	return c.Prefixed(name)
 }
 
-func (c *JetStream) Defaults(generate bool) {
+func (c *JetStream) Defaults(opts DefaultOpts) {
 	c.Addresses = []string{}
 	c.TopicPrefix = "Dendrite"
-	if generate {
+	if opts.Generate {
 		c.StoragePath = Path("./")
 		c.NoLog = true
 		c.DisableTLSValidation = true
diff --git a/setup/config/config_keyserver.go b/setup/config/config_keyserver.go
index 5f2f22c8a..dca9ca9f5 100644
--- a/setup/config/config_keyserver.go
+++ b/setup/config/config_keyserver.go
@@ -3,27 +3,31 @@ package config
 type KeyServer struct {
 	Matrix *Global `yaml:"-"`
 
-	InternalAPI InternalAPIOptions `yaml:"internal_api"`
+	InternalAPI InternalAPIOptions `yaml:"internal_api,omitempty"`
 
-	Database DatabaseOptions `yaml:"database"`
+	Database DatabaseOptions `yaml:"database,omitempty"`
 }
 
-func (c *KeyServer) Defaults(generate bool) {
-	c.InternalAPI.Listen = "http://localhost:7779"
-	c.InternalAPI.Connect = "http://localhost:7779"
-	c.Database.Defaults(10)
-	if generate {
-		c.Database.ConnectionString = "file:keyserver.db"
+func (c *KeyServer) Defaults(opts DefaultOpts) {
+	if !opts.Monolithic {
+		c.InternalAPI.Listen = "http://localhost:7779"
+		c.InternalAPI.Connect = "http://localhost:7779"
+		c.Database.Defaults(10)
+	}
+	if opts.Generate {
+		if !opts.Monolithic {
+			c.Database.ConnectionString = "file:keyserver.db"
+		}
 	}
 }
 
 func (c *KeyServer) Verify(configErrs *ConfigErrors, isMonolith bool) {
-	if c.Matrix.DatabaseOptions.ConnectionString == "" {
-		checkNotEmpty(configErrs, "key_server.database.connection_string", string(c.Database.ConnectionString))
-	}
 	if isMonolith { // polylith required configs below
 		return
 	}
+	if c.Matrix.DatabaseOptions.ConnectionString == "" {
+		checkNotEmpty(configErrs, "key_server.database.connection_string", string(c.Database.ConnectionString))
+	}
 	checkURL(configErrs, "key_server.internal_api.listen", string(c.InternalAPI.Listen))
 	checkURL(configErrs, "key_server.internal_api.connect", string(c.InternalAPI.Connect))
 }
diff --git a/setup/config/config_mediaapi.go b/setup/config/config_mediaapi.go
index 9717aa59e..53a8219eb 100644
--- a/setup/config/config_mediaapi.go
+++ b/setup/config/config_mediaapi.go
@@ -7,12 +7,12 @@ import (
 type MediaAPI struct {
 	Matrix *Global `yaml:"-"`
 
-	InternalAPI InternalAPIOptions `yaml:"internal_api"`
-	ExternalAPI ExternalAPIOptions `yaml:"external_api"`
+	InternalAPI InternalAPIOptions `yaml:"internal_api,omitempty"`
+	ExternalAPI ExternalAPIOptions `yaml:"external_api,omitempty"`
 
 	// The MediaAPI database stores information about files uploaded and downloaded
 	// by local users. It is only accessed by the MediaAPI.
-	Database DatabaseOptions `yaml:"database"`
+	Database DatabaseOptions `yaml:"database,omitempty"`
 
 	// The base path to where the media files will be stored. May be relative or absolute.
 	BasePath Path `yaml:"base_path"`
@@ -38,23 +38,41 @@ type MediaAPI struct {
 // DefaultMaxFileSizeBytes defines the default file size allowed in transfers
 var DefaultMaxFileSizeBytes = FileSizeBytes(10485760)
 
-func (c *MediaAPI) Defaults(generate bool) {
-	c.InternalAPI.Listen = "http://localhost:7774"
-	c.InternalAPI.Connect = "http://localhost:7774"
-	c.ExternalAPI.Listen = "http://[::]:8074"
+func (c *MediaAPI) Defaults(opts DefaultOpts) {
+	if !opts.Monolithic {
+		c.InternalAPI.Listen = "http://localhost:7774"
+		c.InternalAPI.Connect = "http://localhost:7774"
+		c.ExternalAPI.Listen = "http://[::]:8074"
+		c.Database.Defaults(5)
+	}
 	c.MaxFileSizeBytes = DefaultMaxFileSizeBytes
 	c.MaxThumbnailGenerators = 10
-	c.Database.Defaults(5)
-	if generate {
-		c.Database.ConnectionString = "file:mediaapi.db"
+	if opts.Generate {
+		c.ThumbnailSizes = []ThumbnailSize{
+			{
+				Width:        32,
+				Height:       32,
+				ResizeMethod: "crop",
+			},
+			{
+				Width:        96,
+				Height:       96,
+				ResizeMethod: "crop",
+			},
+			{
+				Width:        640,
+				Height:       480,
+				ResizeMethod: "scale",
+			},
+		}
+		if !opts.Monolithic {
+			c.Database.ConnectionString = "file:mediaapi.db"
+		}
 		c.BasePath = "./media_store"
 	}
 }
 
 func (c *MediaAPI) Verify(configErrs *ConfigErrors, isMonolith bool) {
-	if c.Matrix.DatabaseOptions.ConnectionString == "" {
-		checkNotEmpty(configErrs, "media_api.database.connection_string", string(c.Database.ConnectionString))
-	}
 	checkNotEmpty(configErrs, "media_api.base_path", string(c.BasePath))
 	checkPositive(configErrs, "media_api.max_file_size_bytes", int64(c.MaxFileSizeBytes))
 	checkPositive(configErrs, "media_api.max_thumbnail_generators", int64(c.MaxThumbnailGenerators))
@@ -66,6 +84,9 @@ func (c *MediaAPI) Verify(configErrs *ConfigErrors, isMonolith bool) {
 	if isMonolith { // polylith required configs below
 		return
 	}
+	if c.Matrix.DatabaseOptions.ConnectionString == "" {
+		checkNotEmpty(configErrs, "media_api.database.connection_string", string(c.Database.ConnectionString))
+	}
 	checkURL(configErrs, "media_api.internal_api.listen", string(c.InternalAPI.Listen))
 	checkURL(configErrs, "media_api.internal_api.connect", string(c.InternalAPI.Connect))
 	checkURL(configErrs, "media_api.external_api.listen", string(c.ExternalAPI.Listen))
diff --git a/setup/config/config_mscs.go b/setup/config/config_mscs.go
index b992f7152..6d5ff39a5 100644
--- a/setup/config/config_mscs.go
+++ b/setup/config/config_mscs.go
@@ -10,13 +10,17 @@ type MSCs struct {
 	// 'msc2946': Spaces Summary - https://github.com/matrix-org/matrix-doc/pull/2946
 	MSCs []string `yaml:"mscs"`
 
-	Database DatabaseOptions `yaml:"database"`
+	Database DatabaseOptions `yaml:"database,omitempty"`
 }
 
-func (c *MSCs) Defaults(generate bool) {
-	c.Database.Defaults(5)
-	if generate {
-		c.Database.ConnectionString = "file:mscs.db"
+func (c *MSCs) Defaults(opts DefaultOpts) {
+	if !opts.Monolithic {
+		c.Database.Defaults(5)
+	}
+	if opts.Generate {
+		if !opts.Monolithic {
+			c.Database.ConnectionString = "file:mscs.db"
+		}
 	}
 }
 
@@ -31,6 +35,9 @@ func (c *MSCs) Enabled(msc string) bool {
 }
 
 func (c *MSCs) Verify(configErrs *ConfigErrors, isMonolith bool) {
+	if isMonolith { // polylith required configs below
+		return
+	}
 	if c.Matrix.DatabaseOptions.ConnectionString == "" {
 		checkNotEmpty(configErrs, "mscs.database.connection_string", string(c.Database.ConnectionString))
 	}
diff --git a/setup/config/config_roomserver.go b/setup/config/config_roomserver.go
index bd6aa1167..5e3b7f2ec 100644
--- a/setup/config/config_roomserver.go
+++ b/setup/config/config_roomserver.go
@@ -3,27 +3,31 @@ package config
 type RoomServer struct {
 	Matrix *Global `yaml:"-"`
 
-	InternalAPI InternalAPIOptions `yaml:"internal_api"`
+	InternalAPI InternalAPIOptions `yaml:"internal_api,omitempty"`
 
-	Database DatabaseOptions `yaml:"database"`
+	Database DatabaseOptions `yaml:"database,omitempty"`
 }
 
-func (c *RoomServer) Defaults(generate bool) {
-	c.InternalAPI.Listen = "http://localhost:7770"
-	c.InternalAPI.Connect = "http://localhost:7770"
-	c.Database.Defaults(10)
-	if generate {
-		c.Database.ConnectionString = "file:roomserver.db"
+func (c *RoomServer) Defaults(opts DefaultOpts) {
+	if !opts.Monolithic {
+		c.InternalAPI.Listen = "http://localhost:7770"
+		c.InternalAPI.Connect = "http://localhost:7770"
+		c.Database.Defaults(20)
+	}
+	if opts.Generate {
+		if !opts.Monolithic {
+			c.Database.ConnectionString = "file:roomserver.db"
+		}
 	}
 }
 
 func (c *RoomServer) Verify(configErrs *ConfigErrors, isMonolith bool) {
-	if c.Matrix.DatabaseOptions.ConnectionString == "" {
-		checkNotEmpty(configErrs, "room_server.database.connection_string", string(c.Database.ConnectionString))
-	}
 	if isMonolith { // polylith required configs below
 		return
 	}
+	if c.Matrix.DatabaseOptions.ConnectionString == "" {
+		checkNotEmpty(configErrs, "room_server.database.connection_string", string(c.Database.ConnectionString))
+	}
 	checkURL(configErrs, "room_server.internal_api.listen", string(c.InternalAPI.Listen))
 	checkURL(configErrs, "room_server.internal_ap.connect", string(c.InternalAPI.Connect))
 }
diff --git a/setup/config/config_syncapi.go b/setup/config/config_syncapi.go
index 7d5e3808a..4e302ae09 100644
--- a/setup/config/config_syncapi.go
+++ b/setup/config/config_syncapi.go
@@ -3,31 +3,35 @@ package config
 type SyncAPI struct {
 	Matrix *Global `yaml:"-"`
 
-	InternalAPI InternalAPIOptions `yaml:"internal_api"`
-	ExternalAPI ExternalAPIOptions `yaml:"external_api"`
+	InternalAPI InternalAPIOptions `yaml:"internal_api,omitempty"`
+	ExternalAPI ExternalAPIOptions `yaml:"external_api,omitempty"`
 
-	Database DatabaseOptions `yaml:"database"`
+	Database DatabaseOptions `yaml:"database,omitempty"`
 
 	RealIPHeader string `yaml:"real_ip_header"`
 }
 
-func (c *SyncAPI) Defaults(generate bool) {
-	c.InternalAPI.Listen = "http://localhost:7773"
-	c.InternalAPI.Connect = "http://localhost:7773"
-	c.ExternalAPI.Listen = "http://localhost:8073"
-	c.Database.Defaults(10)
-	if generate {
-		c.Database.ConnectionString = "file:syncapi.db"
+func (c *SyncAPI) Defaults(opts DefaultOpts) {
+	if !opts.Monolithic {
+		c.InternalAPI.Listen = "http://localhost:7773"
+		c.InternalAPI.Connect = "http://localhost:7773"
+		c.ExternalAPI.Listen = "http://localhost:8073"
+		c.Database.Defaults(20)
+	}
+	if opts.Generate {
+		if !opts.Monolithic {
+			c.Database.ConnectionString = "file:syncapi.db"
+		}
 	}
 }
 
 func (c *SyncAPI) Verify(configErrs *ConfigErrors, isMonolith bool) {
-	if c.Matrix.DatabaseOptions.ConnectionString == "" {
-		checkNotEmpty(configErrs, "sync_api.database", string(c.Database.ConnectionString))
-	}
 	if isMonolith { // polylith required configs below
 		return
 	}
+	if c.Matrix.DatabaseOptions.ConnectionString == "" {
+		checkNotEmpty(configErrs, "sync_api.database", string(c.Database.ConnectionString))
+	}
 	checkURL(configErrs, "sync_api.internal_api.listen", string(c.InternalAPI.Listen))
 	checkURL(configErrs, "sync_api.internal_api.connect", string(c.InternalAPI.Connect))
 	checkURL(configErrs, "sync_api.external_api.listen", string(c.ExternalAPI.Listen))
diff --git a/setup/config/config_userapi.go b/setup/config/config_userapi.go
index d1e2b7fe1..97a6d738b 100644
--- a/setup/config/config_userapi.go
+++ b/setup/config/config_userapi.go
@@ -5,7 +5,7 @@ import "golang.org/x/crypto/bcrypt"
 type UserAPI struct {
 	Matrix *Global `yaml:"-"`
 
-	InternalAPI InternalAPIOptions `yaml:"internal_api"`
+	InternalAPI InternalAPIOptions `yaml:"internal_api,omitempty"`
 
 	// The cost when hashing passwords.
 	BCryptCost int `yaml:"bcrypt_cost"`
@@ -18,30 +18,34 @@ type UserAPI struct {
 
 	// The Account database stores the login details and account information
 	// for local users. It is accessed by the UserAPI.
-	AccountDatabase DatabaseOptions `yaml:"account_database"`
+	AccountDatabase DatabaseOptions `yaml:"account_database,omitempty"`
 }
 
 const DefaultOpenIDTokenLifetimeMS = 3600000 // 60 minutes
 
-func (c *UserAPI) Defaults(generate bool) {
-	c.InternalAPI.Listen = "http://localhost:7781"
-	c.InternalAPI.Connect = "http://localhost:7781"
+func (c *UserAPI) Defaults(opts DefaultOpts) {
+	if !opts.Monolithic {
+		c.InternalAPI.Listen = "http://localhost:7781"
+		c.InternalAPI.Connect = "http://localhost:7781"
+		c.AccountDatabase.Defaults(10)
+	}
 	c.BCryptCost = bcrypt.DefaultCost
 	c.OpenIDTokenLifetimeMS = DefaultOpenIDTokenLifetimeMS
-	c.AccountDatabase.Defaults(10)
-	if generate {
-		c.AccountDatabase.ConnectionString = "file:userapi_accounts.db"
+	if opts.Generate {
+		if !opts.Monolithic {
+			c.AccountDatabase.ConnectionString = "file:userapi_accounts.db"
+		}
 	}
 }
 
 func (c *UserAPI) Verify(configErrs *ConfigErrors, isMonolith bool) {
 	checkPositive(configErrs, "user_api.openid_token_lifetime_ms", c.OpenIDTokenLifetimeMS)
-	if c.Matrix.DatabaseOptions.ConnectionString == "" {
-		checkNotEmpty(configErrs, "user_api.account_database.connection_string", string(c.AccountDatabase.ConnectionString))
-	}
 	if isMonolith { // polylith required configs below
 		return
 	}
+	if c.Matrix.DatabaseOptions.ConnectionString == "" {
+		checkNotEmpty(configErrs, "user_api.account_database.connection_string", string(c.AccountDatabase.ConnectionString))
+	}
 	checkURL(configErrs, "user_api.internal_api.listen", string(c.InternalAPI.Listen))
 	checkURL(configErrs, "user_api.internal_api.connect", string(c.InternalAPI.Connect))
 }
diff --git a/setup/mscs/msc2836/msc2836_test.go b/setup/mscs/msc2836/msc2836_test.go
index 3e9d90a1f..0388fcc53 100644
--- a/setup/mscs/msc2836/msc2836_test.go
+++ b/setup/mscs/msc2836/msc2836_test.go
@@ -547,7 +547,10 @@ func (r *testRoomserverAPI) QueryMembershipForUser(ctx context.Context, req *roo
 func injectEvents(t *testing.T, userAPI userapi.UserInternalAPI, rsAPI roomserver.RoomserverInternalAPI, events []*gomatrixserverlib.HeaderedEvent) *mux.Router {
 	t.Helper()
 	cfg := &config.Dendrite{}
-	cfg.Defaults(true)
+	cfg.Defaults(config.DefaultOpts{
+		Generate:   true,
+		Monolithic: true,
+	})
 	cfg.Global.ServerName = "localhost"
 	cfg.MSCs.Database.ConnectionString = "file:msc2836_test.db"
 	cfg.MSCs.MSCs = []string{"msc2836"}
diff --git a/test/testrig/base.go b/test/testrig/base.go
index 33230921c..9747ea600 100644
--- a/test/testrig/base.go
+++ b/test/testrig/base.go
@@ -30,12 +30,21 @@ import (
 
 func CreateBaseDendrite(t *testing.T, dbType test.DBType) (*base.BaseDendrite, func()) {
 	var cfg config.Dendrite
-	cfg.Defaults(false)
+	cfg.Defaults(config.DefaultOpts{
+		Generate:   false,
+		Monolithic: true,
+	})
 	cfg.Global.JetStream.InMemory = true
 	switch dbType {
 	case test.DBTypePostgres:
-		cfg.Global.Defaults(true)   // autogen a signing key
-		cfg.MediaAPI.Defaults(true) // autogen a media path
+		cfg.Global.Defaults(config.DefaultOpts{ // autogen a signing key
+			Generate:   true,
+			Monolithic: true,
+		})
+		cfg.MediaAPI.Defaults(config.DefaultOpts{ // autogen a media path
+			Generate:   true,
+			Monolithic: true,
+		})
 		cfg.Global.ServerName = "test"
 		// use a distinct prefix else concurrent postgres/sqlite runs will clash since NATS will use
 		// the file system event with InMemory=true :(
@@ -49,7 +58,10 @@ func CreateBaseDendrite(t *testing.T, dbType test.DBType) (*base.BaseDendrite, f
 		}
 		return base.NewBaseDendrite(&cfg, "Test", base.DisableMetrics), close
 	case test.DBTypeSQLite:
-		cfg.Defaults(true) // sets a sqlite db per component
+		cfg.Defaults(config.DefaultOpts{
+			Generate:   true,
+			Monolithic: false, // because we need a database per component
+		})
 		cfg.Global.ServerName = "test"
 		// use a distinct prefix else concurrent postgres/sqlite runs will clash since NATS will use
 		// the file system event with InMemory=true :(
@@ -82,7 +94,10 @@ func CreateBaseDendrite(t *testing.T, dbType test.DBType) (*base.BaseDendrite, f
 func Base(cfg *config.Dendrite) (*base.BaseDendrite, nats.JetStreamContext, *nats.Conn) {
 	if cfg == nil {
 		cfg = &config.Dendrite{}
-		cfg.Defaults(true)
+		cfg.Defaults(config.DefaultOpts{
+			Generate:   true,
+			Monolithic: true,
+		})
 	}
 	cfg.Global.JetStream.InMemory = true
 	base := base.NewBaseDendrite(cfg, "Tests")