Systems and methods for extending a container orchestration engine API in-process are disclosed. A processing device may compile each of one or more custom resource definition (CRD) controllers that are created in a cluster at run-time into a respective isolation module to generate one or more isolation modules, wherein the one or more isolation modules are all hosted in a service. The processing device may monitor for application program interface (API) events serviced by each of the one or more CRD controllers and in response to detecting an API event serviced by a CRD controller of the one or more CRD controllers, executing a respective isolation module of the CRD controller.