A security system scans application programming interfaces (APIs) to detect security vulnerabilities by receiving API documentation from a third-party system associated with the API and organizing it in an API specification that describes the hostname of the API and one or more endpoints of the API. For each of the endpoints, the API specification includes a uniform resource identifier, a method term, an input content type, an output content type (if applicable), authorization details, and any associated parameters or arguments. The security system performs an audit job for each combination of endpoints, potential security vulnerabilities, and (in some embodiments) authentication flows. In some embodiments, the security system is able to access portions of the API requiring authentication by using authentication flows received from the third-party system and detect security vulnerabilities related to authentication by manipulating the authentication units that make up the authentication flow.