Measurement of the permeability of microcapsules with Fluorescence Recovery After Photobleaching (FRAP) enables analysis of individual microcapsules, the study of their batch heterogeneity, and the survey of changes in an individual capsule's transport properties under different environmental conditions. We present a modified protocol and analysis which expands the parameter space of microcapsule sizes and permeabilities that can be accurately measured with FRAP. Simulations and experiments show that the hybrid analysis, which accounts for both permeation through the shell and free diffusion, precisely captures the kinetics of typical fluorescence recovery curves. The modified approach eliminates the need for painstaking controls to determine the FRAP measurement volume and the spatial distribution of bleached tracers, while accurately extracting the permeability of the microcapsule from FRAP data acquired using a straightforward procedure.