The mechanism of active pharmaceutical ingredient (API) mobility during release in microparticle formulation was investigated using periodically structured illumination combined with spatial Fourier transform fluorescence recovery after photobleaching (FT-FRAP). FT-FRAP applies structured photobleaching across a given field of view, allowing for the monitoring of molecular mobility through the analysis of recovery patterns in the FT domain. Encoding molecular mobility in the FT domain offers several advantages, including improved signal-to-noise ratio, simplified mathematical calculations, reduced sampling requirements, compatibility with multiphoton microscopy for imaging API molecules within the formulations, and the ability to distinguish between exchange and diffusion processes. To prepare microparticles for FT-FRAP analysis, a homogeneous mixture of dipyridamole and pH-independent methyl methacrylate polymer (Eudragit RS and RL) was processed using laminar jet breakup induced by vibration in a frequency-driven encapsulator. The encapsulated microparticles were characterized based on particle size distribution, encapsulation efficiency, batch size, and morphology. Utilizing FT-FRAP, the internal diffusion and exchange molecular mobility within RL and RS microparticles were discriminated and quantified. Theoretical modeling of exchange- and diffusion-controlled release revealed that both RL and RS microparticles exhibited similar exchange decay rates, but RL displayed a significantly higher diffusion coefficient. This difference in diffusion within RL and RS microparticles was correlated with their macroscopic dissolution performance.