Interfacial polymerization techniques offer a versatile route for microcapsule synthesis. We designed a microfluidic process to synthesize monodisperse polyurea microcapsules (PUMCs); the microcapsules are formed by an interfacial polymerization of isocyanate dissolved in the oil and an amine dissolved in water. We measure the mechanical properties of the capsule as well as transport properties through the membrane using two microfluidic methods. We show that the elasticity and the permeability of the shell are controlled by surfactant additives, added during the synthesis. The control of the nanostructure of the shell by surfactants provides new means to design encapsulation systems with tailored mechanical and physicochemical properties.