Oral therapy utilizing cell microencapsulation has shown promise in the treatment of many diseases. Current obtainable microcapsule membranes, however, show inadequate stability in the gastrointestinal (GI) environment, thus restricting the general application of live cells for oral therapy. To overcome this limitation, we have previously developed a novel multilayer alginate/poly-L-lysine/pectin/poly-L-lysine/alginate microcapsule (APPPA) with demonstrated improvement on membrane stability over the frequently reported alginate/poly-L-lysine/alginate (APA) microcapsules. In this study, we further examined the effects of preparation conditions on microcapsule formation, and assessed the membrane strength and GI stability. Results showed that increased membrane strength of the APPPA microcapsules was attained by using pectin with low degree of esterification as the mid-layer material, saline as the solvent for the preparation solutions and washing medium, and 0.1 M CaCl2 as the gelling solution for alginate cores. Resistance of this membrane to the simulated GI fluids was also investigated. Permeability of and release profiles from the APPPA microcapsules were found comparable to the APA microcapsules. These findings suggested that the multi-layer APPPA microcapsule formulation may have potential in oral delivery of proteins, live bacterial cells and other biomedical applications.