A number of new platforms have been developed for multiplexed bioassays that rely on imaging targeted fluorescent beads labeled with different fluorescent dyes. We developed a compact, low-cost three-dimensional printed fluorescence microscope that can be used as a detector for mutiplexed, bead-based assays to support point-of-care applications. Images obtained with the microscope were analyzed to differentiate multiple analytes in a single sample with a comparable limit of detection to commercially available macroscopic assay platforms.