The fight against nosocomial infections in hospitals, has promoted the use of microencapsulated essential oils on medical wearing uniforms. These types of microcapsules can be improved with the use of antimicrobial polymers in the shell structure. Chitosan is one of the most used biopolymers and the effectiveness of the treatment can be increased with the combination of different molecular weight chains of chitosan. This modification in the composition of shell structure allows controlling the rate of hydrolysis and, therefore the amount of its cationic form. The main objective of this work is to define a methodology to get microcapsules with different shell compositions, using surfactants as stabilizers in their first step. Once they have been obtained, these microcapsules will be fixed into textile substrates with the objective to use these tissues as surgical and medical clothes to spread the antibacterial effect, in sanitary staff, as well as in the own patient. In the process of microencapsulation the molecular weight distribution of polymers, influences strongly the delivery mechanisms of the active principle, as well as the chemical characteristics of the textile substrate used in every case. In this work, several chitosan biopolymers have been checked. Structural changes in the stabilization first step and the influence of the cross-linking extension have been related with the final antibacterial effect when fixed on cotton substrates.