diff --git a/libs/ardour/ardour/session.h b/libs/ardour/ardour/session.h
index 519d614248..8aae4d5879 100644
--- a/libs/ardour/ardour/session.h
+++ b/libs/ardour/ardour/session.h
@@ -1528,6 +1528,8 @@ class LIBARDOUR_API Session : public PBD::StatefulDestructible, public PBD::Scop
 	AutoConnectQueue _auto_connect_queue;
 	guint _latency_recompute_pending;
 
+	void get_physical_ports (std::vector<std::string>& inputs, std::vector<std::string>& outputs, DataType type, bool excluding);
+
 	void auto_connect (const AutoConnectRequest&);
 	void queue_latency_recompute ();
 
diff --git a/libs/ardour/session.cc b/libs/ardour/session.cc
index b22fe03643..431cadfca0 100644
--- a/libs/ardour/session.cc
+++ b/libs/ardour/session.cc
@@ -910,6 +910,41 @@ Session::setup_click_state (const XMLNode* node)
 	}
 }
 
+void
+Session::get_physical_ports (vector<string>& inputs, vector<string>& outputs, DataType type, bool excluding)
+{
+	_engine.get_physical_inputs (type, inputs);
+
+	if (excluding) {
+		/* rip out ControlOnly ports, and ALSA MIDI Through ports */
+
+		for (vector<string>::iterator si = inputs.begin(); si != inputs.end(); ) {
+			if (PortManager::port_is_control_only (*si)) {
+				si = inputs.erase (si);
+			} else if ((*si).find (X_("Midi Through")) != string::npos || (*si).find (X_("Midi-Through")) != string::npos) {
+				si = inputs.erase (si);
+			} else {
+				++si;
+			}
+		}
+	}
+	_engine.get_physical_outputs (type, outputs);
+
+	if (excluding) {
+		/* rip out ControlOnly ports, and ALSA MIDI Through ports */
+
+		for (vector<string>::iterator si = outputs.begin(); si != outputs.end(); ) {
+			if (PortManager::port_is_control_only (*si)) {
+				si = outputs.erase (si);
+			} else if ((*si).find (X_("Midi Through")) != string::npos || (*si).find (X_("Midi-Through")) != string::npos) {
+				si = outputs.erase (si);
+			} else {
+				++si;
+			}
+		}
+	}
+}
+
 void
 Session::setup_bundles ()
 {
@@ -928,30 +963,9 @@ Session::setup_bundles ()
 
 	vector<string> inputs[DataType::num_types];
 	vector<string> outputs[DataType::num_types];
+
 	for (uint32_t i = 0; i < DataType::num_types; ++i) {
-		_engine.get_physical_inputs (DataType (DataType::Symbol (i)), inputs[i]);
-
-		/* rip out ControlOnly ports */
-
-		for (vector<string>::iterator si = inputs[i].begin(); si != inputs[i].end(); ) {
-			if (PortManager::port_is_control_only (*si)) {
-				si = inputs[i].erase (si);
-			} else {
-				++si;
-			}
-		}
-
-		_engine.get_physical_outputs (DataType (DataType::Symbol (i)), outputs[i]);
-
-		/* rip out ControlOnly ports */
-
-		for (vector<string>::iterator si = outputs[i].begin(); si != outputs[i].end(); ) {
-			if (PortManager::port_is_control_only (*si)) {
-				si = outputs[i].erase (si);
-			} else {
-				++si;
-			}
-		}
+		get_physical_ports (inputs[i], outputs[i], DataType (DataType::Symbol (i)), true);
 	}
 
 	/* Create a set of Bundle objects that map
@@ -6934,8 +6948,7 @@ Session::auto_connect (const AutoConnectRequest& ar)
 		vector<string> physinputs;
 		vector<string> physoutputs;
 
-		_engine.get_physical_outputs (*t, physoutputs);
-		_engine.get_physical_inputs (*t, physinputs);
+		get_physical_ports (physinputs, physoutputs, *t, true);
 
 		if (!physinputs.empty() && ar.connect_inputs) {
 			uint32_t nphysical_in = physinputs.size();