Techniques are described for controlling an autonomous vehicle such as an unmanned aerial vehicle (UAV) using objective-based inputs. In an embodiment, the underlying functionality of an autonomous navigation system is exposed via an application programming interface (API) allowing the UAV to be controlled through specifying a behavioral objective, for example, using a call to the API to set parameters for the behavioral objective. The autonomous navigation system can then incorporate perception inputs such as sensor data from sensors mounted to the UAV and the set parameters using a multi-objective motion planning process to generate a proposed trajectory that most closely satisfies the behavioral objective in view of certain constraints. In some embodiments, developers can utilize the API to build customized applications for the UAV. Such applications, also referred to as “skills,” can be developed, shared, and executed to control behavior of an autonomous UAV and aid in overall system improvement.