The present invention extends to methods, systems, and computer program products for integrating messaging diagnostics into a messaging pipeline. A messaging pipeline receives a control message and passes the control message through one or more pipeline components (potentially a security component) positioned in the messaging pipeline. The control message is passed to a diagnostic control component positioned in the messaging pipeline subsequent to passing the received control message through one or more pipeline components. The diagnostic control component activates message diagnostics at diagnostic components positioned within one or more messaging pipelines in accordance with instructions contained in the control message. When message diagnostics are activated, messaging pipelines pass accessed messages to diagnostic components positioned in the messaging pipeline. The diagnostic components perform diagnostic operations based on the contents of the accessed message in accordance with instructions contained in the previously processed (and potentially authenticated) control message.