Functional materials with antimicrobial properties are being investigated in order to provide shoes with new properties and added value by incorporating natural antimicrobial agents to conventional materials (leather, fabrics, foams, etc). Microencapsulation is an effective method to protect these functional natural biocides from reactions with moisture, light, and oxygen. If a footwear material is treated with microencapsulated biocide agents, higher durability of functionality is expected. This article reports the evaluation of Melaleuca alternifolia (tea tree) oil which is a natural essential oil, as an antimicrobial agent for footwear application. Furthermore, microcapsules containing this essential oil were synthesized by in situ polymerization method using a melamine-formaldehyde resin as shell material in order to increase the durability of this natural biocide in footwear materials. Microcapsule characterization, such as particle size, morphology, and chemical properties was carried out for different oil to polymer ratios. Finally, the incorporation of the microencapsulated biocides into different footwear materials was also evaluated.