Implementations set forth herein relate to an automated assistant that can operate as an interface between a user and a separate application to search application content of the separate application. The automated assistant can interact with existing search filter features of another application and can also adapt in circumstances when certain filter parameters are not directly controllable at a search interface of the application. For instance, when a user requests that a search operation be performed using certain terms, those terms may refer to content filters that may not be available at a search interface of the application. However, the automated assistant can generate an assistant input based on those content filters in order to ensure that any resulting search results will be filtered accordingly. The assistant input can then be submitted into a search field of the application and a search operation can be executed.