A substrate processing apparatus is provided. The apparatus includes an imaging unit that images a mark on a substrate, and a processor that aligns the substrate based on an image of the mark obtained by the imaging unit. If the alignment has failed, the processor identifies a factor of the failure based on information including the image and executes at least one of a plurality of recovery processes based on the identified factor. The processor includes an output unit that outputs a condition for the at least one of recovery processes in accordance with an inference model, and a learning unit that learns the inference model based on an execution result of the at least one of the recovery processes under the condition output from the output unit.