diff --git a/test/functional/p2p_timeouts.py b/test/functional/p2p_timeouts.py
index a308577c02087..b4fa5099d8758 100755
--- a/test/functional/p2p_timeouts.py
+++ b/test/functional/p2p_timeouts.py
@@ -68,11 +68,14 @@ def run_test(self):
 
         with self.nodes[0].assert_debug_log(['Unsupported message "ping" prior to verack from peer=0']):
             no_verack_node.send_message(msg_ping())
-        with self.nodes[0].assert_debug_log(['non-version message before version handshake. Message "ping" from peer=1']):
-            no_version_node.send_message(msg_ping())
 
-        self.mock_forward(1)
+        # With v2, non-version messages before the handshake would be interpreted as part of the key exchange.
+        # Therefore, don't execute this part of the test if v2transport is chosen.
+        if not self.options.v2transport:
+            with self.nodes[0].assert_debug_log(['non-version message before version handshake. Message "ping" from peer=1']):
+                no_version_node.send_message(msg_ping())
 
+        self.mock_forward(1)
         assert "version" in no_verack_node.last_message
 
         assert no_verack_node.is_connected
@@ -80,11 +83,12 @@ def run_test(self):
         assert no_send_node.is_connected
 
         no_verack_node.send_message(msg_ping())
-        no_version_node.send_message(msg_ping())
+        if not self.options.v2transport:
+            no_version_node.send_message(msg_ping())
 
         expected_timeout_logs = [
             "version handshake timeout peer=0",
-            "socket no message in first 3 seconds, 1 0 peer=1",
+            f"socket no message in first 3 seconds, {'0' if self.options.v2transport else '1'} 0 peer=1",
             "socket no message in first 3 seconds, 0 0 peer=2",
         ]
 
@@ -100,5 +104,6 @@ def run_test(self):
             extra_args=['-peertimeout=0'],
         )
 
+
 if __name__ == '__main__':
     TimeoutsTest().main()
diff --git a/test/functional/test_runner.py b/test/functional/test_runner.py
index 320e0abf1008f..a93544259554d 100755
--- a/test/functional/test_runner.py
+++ b/test/functional/test_runner.py
@@ -153,6 +153,7 @@
     'p2p_invalid_messages.py',
     'rpc_createmultisig.py',
     'p2p_timeouts.py',
+    'p2p_timeouts.py --v2transport',
     'wallet_dump.py --legacy-wallet',
     'rpc_signer.py',
     'wallet_signer.py --descriptors',