One variation of a method for autonomously training an animal includes: loading an autonomous training protocol for the animal onto a training apparatus configured to dispense units of a primary reinforcer responsive to behaviors performed by the animal; during an autonomous training session for the animal, accessing a video feed of a working field near the training apparatus, detecting the animal in the video feed, and executing the first autonomous training protocol; calculating a training score for the autonomous training session based on behaviors performed by the animal during the autonomous training session; selecting a manual training protocol, from a set of manual training protocols, based on the training score; generating a prompt to execute the first manual training protocol with the animal during a first manual training session; and transmitting the prompt to a user associated with the animal.