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There is a need for better understanding of the biocompatibility of alginate–polycation microcapsules based on their physicochemical characteristics. Microcapsules composed of alginate with 44% (IntG) or 71% (HiG) guluronate, gelled with calcium (Ca) or barium (Ba) and coated with poly-L-lysine (PLL) or poly-L-ornithine (PLO), followed by IntG alginate were compared. For microcapsules with an IntG(Ca) gel core, using PLO instead of PLL resulted in less immune cell adhesion after 2 days in C57BL/6J mice. The PLO microcapsules were also characterized by greater hydrophilicity and superior resistance to swelling and damage under osmotic stress. For microcapsules with a PLL membrane, replacing the IntG(Ca) gel core with IntG(Ba) or HiG(Ca) gel resulted in stronger immune responses (p < 0.05). This was explained by poor penetration of PLL into the gel, as demonstrated by Fourier transform infrared spectroscopy analyses and membrane rupturing during osmotic swelling. X-ray photoelectron spectroscopy analyses show that all microcapsules had the same amount of polycation at their surface. Moreover, alginate coatings had non-significant effects on the biocompatibility and physicochemical properties of the microcapsules. Thus, alginate–polycation interactions for membrane formation are more important for biocompatibility than either the quantity of polycation at the surface or the alginate coating.