diff --git a/synapse/federation/transaction_queue.py b/synapse/federation/transaction_queue.py
index 94d7423d01..8cbf8c4f7f 100644
--- a/synapse/federation/transaction_queue.py
+++ b/synapse/federation/transaction_queue.py
@@ -463,7 +463,19 @@ class TransactionQueue(object):
                 # pending_transactions flag.
 
                 pending_pdus = self.pending_pdus_by_dest.pop(destination, [])
+
+                # We can only include at most 50 PDUs per transactions
+                pending_pdus, leftover_pdus = pending_pdus[:50], pending_pdus[50:]
+                if leftover_pdus:
+                    self.pending_pdus_by_dest[destination] = leftover_pdus
+
                 pending_edus = self.pending_edus_by_dest.pop(destination, [])
+
+                # We can only include at most 100 EDUs per transactions
+                pending_edus, leftover_edus = pending_edus[:100], pending_edus[100:]
+                if leftover_edus:
+                    self.pending_edus_by_dest[destination] = leftover_edus
+
                 pending_presence = self.pending_presence_by_dest.pop(destination, {})
 
                 pending_edus.extend(