Biomolecular condensates are important targets of investigation due to their physiological functions as well as their roles in neurodegenerative diseases, cancer, and drug delivery. Here, we present a protocol for characterizing biomolecular condensates across three confocal microscopy-based modalities, namely, subcellular localization, fluorescent recovery after photobleaching (FRAP), and time lapse analysis of mobility and fission/fusion events. We detail optimized image acquisition parameters and describe steps for analysis workflows utilizing ImageJ macros and plugins, including 2D and 3D analysis approaches.