An agent installed on application server having a WSGI web application dynamically instruments that web application. The agent may modify the application via instrumentation such that it can be monitored without specific details of the WSGI application framework. A configuration file may be modified upon detecting a call to the application configuration file through a gateway interface that receives the call. After modifying the configuration file, the modified configuration file is executed in response to the call. Additionally, for subsequent calls to that particular web application, the WSGI gateway will call the modified WSGI configuration file for execution instead of the original WSGI file.