The formation of new microcapsules based on polyelectrolyte complexes between carrageenans and oligochitosan has been investigated. The optimization of the process, which includes the selection of the most suitable solvent and investigation of the influence of reaction conditions on capsule properties, is presented. Iota-carrageenan (1.2–2% wt.) prepared in HEPES buffer was found to be the most suitable for the formation of mechanically stable capsules. These new capsules combine extremely high deformability (>90%) and elasticity with permeability control and can be applied in various bioencapsulation technologies. It has been shown that the reaction time influences the mechanical properties, whereas carrageenan concentration and the temperature during the capsule formation effect both mechanical and porosity characteristic of the membrane. Moreover, the temperature influences the kinetics of the diffusion through the complex iota-carrageenan/oligochitosan membrane. In general egress is faster above the sol–gel transition point, indicating applicability in thermo-induced releasing systems.