diff --git a/.changeset/patch-clean-mcp-config.md b/.changeset/patch-clean-mcp-config.md
new file mode 100644
index 0000000000..f5f72074a0
--- /dev/null
+++ b/.changeset/patch-clean-mcp-config.md
@@ -0,0 +1,5 @@
+---
+"gh-aw": patch
+---
+
+Gateway startup now removes `/home/runner/.copilot/mcp-config.json` after configuring the MCP server so the temporary config isn't left on disk.
diff --git a/actions/setup/sh/start_mcp_gateway.sh b/actions/setup/sh/start_mcp_gateway.sh
index accd64aa22..3c282df6b2 100755
--- a/actions/setup/sh/start_mcp_gateway.sh
+++ b/actions/setup/sh/start_mcp_gateway.sh
@@ -413,6 +413,16 @@ else
 fi
 echo ""
 
+# Delete MCP server configuration file after gateway is launched
+echo "Cleaning up MCP server configuration file..."
+if [ -f /home/runner/.copilot/mcp-config.json ]; then
+  rm /home/runner/.copilot/mcp-config.json
+  echo "MCP server configuration file deleted"
+else
+  echo "MCP server configuration file not found (already deleted or never created)"
+fi
+echo ""
+
 echo "MCP gateway is running:"
 echo "  - From host: http://localhost:${MCP_GATEWAY_PORT}"
 echo "  - From containers: http://${MCP_GATEWAY_DOMAIN}:${MCP_GATEWAY_PORT}"