Design and characterisation of capsules is not an easy task owing to the multiple involved preparation factors and parameters. Here, a novel method to characterise capsule membrane permeability to solute molecules by an inverse approach is proposed. Transport of chemical species between the capsule core and the surrounding medium through the membrane is described by the Fick's second law with a position-dependent diffusion coefficient. Solutions are computed in spherical coordinates using a finite difference scheme developed for diffusion in multilayer configuration. They are validated using semi-analytical solutions and fully three-dimensional lattice Boltzmann simulations. As a proof of concept, the method is applied to experimental data available in the literature on the kinetics of glucose release and absorption to determine the membrane permeability of capsules. The proposed method is easy to use and determines correctly the permeability of capsule membranes for controlled drug release and absorption applications.