diff --git a/docs/toolhive/guides-cli/run-mcp-servers.mdx b/docs/toolhive/guides-cli/run-mcp-servers.mdx
index b52a9868..40b47479 100644
--- a/docs/toolhive/guides-cli/run-mcp-servers.mdx
+++ b/docs/toolhive/guides-cli/run-mcp-servers.mdx
@@ -805,6 +805,13 @@ This creates a new server instance with identical settings to the original. If
 the original server used secrets, you must have the same secrets available in
 your ToolHive secrets store.
 
+:::note
+
+When you use `--from-config`, you cannot specify any other command-line flags.
+The configuration file must contain all server settings.
+
+:::
+
 ## Next steps
 
 See [Monitor and manage MCP servers](./manage-mcp-servers.md) to monitor and