The present invention provides a method for detecting microorganisms, comprising an imaging step in which a membrane filter that filters a liquid is attached to a surface of a plate medium and cultured for a predetermined period of time, followed by peeling from the plate medium and fluorescently staining to capture fluorescence images; a learning data generation step of inputting, for each of the plurality of the fluorescence images, microorganism position information indicating the microorganism positions on the fluorescence images to generate, as learning data, the fluorescence images and the microorganism position information; a step of generating a trained model by performing machine learning based on the learning data; and a step of determining the presence or absence of microorganisms using the trained model for the fluorescence images input as an inspection target, and the like.