In order to characterize the mechanical properties of bioartificial microcapsules, we have designed an inverse analysis technique that combines microfluidic experiments with a multi-physical numerical model. The experiments consist of flowing a suspension of capsules in a channel with cross section similar to the particle size. The mechanical properties of the capsule membrane are deduced from the deformed shape by means of a fluid-structure interaction model of the problem. The model couples a boundary integral method to solve for the inner and outer fluid motion with a collocation method to solve for the membrane deformation. An optimization technique is used to find the parameters that provide the same deformation as measured experimentally and deduce an estimation of the membrane properties. The technique is applied on capsules with reticulated protein membranes.We show that it is possible to discriminate the influence of the physico-chemical conditions of fabrication.