Various embodiments include methods for protecting a web application server from non-benign web application usage. Embodiment methods may include receiving from a client device a service request message that includes information suitable for causing a web application operating on the web application server to perform one or more operations. In response, a processor, such as within the web application server or another network device, may analyze usage of the web application by the client device via a combination of a honeypot component, a sandboxed detonator component, and a Web Application Firewall (WAF) component. Analysis results may be generated by analyzing the received service request message or a server response message sent by the web application server. The analysis results may be used to identify non-benign web application usage. Actions may be taken to protect the web application server and/or the client device from the identified non-benign web application usage.