We employed microemulsion combined with the solvent evaporation technique to produce biodegradable polycaprolactone (PCL) MCs, containing encapsulated isophorone diisocyanate (IPDI), to act as crosslinkers in high-performance adhesive formulations. The MC production process was optimized by applying a design of experiment (DoE) statistical approach, aimed at decreasing the MCs’ average size. For that, three different factors were considered, namely the concentration of two emulsifiers, polyvinyl alcohol (PVA) and gum arabic (GA); and the oil-to-water phase ratio of the emulsion. The significance of each factor was evaluated, and a predictive model was developed. We were able to decrease the average MC size from 326 μm to 70 µm, maintaining a high encapsulation yield of approximately 60% of the MCs’ weight, and a very satisfactory shelf life. The MCs’ average size optimization enabled us to obtain an improved distributive and dispersive mixture of isocyanate-loaded MCs at the adhesive bond. The MCs’ suitability as crosslinkers for footwear adhesives was assessed following industry standards. Peel tests revealed peel strength values above the minimum required for casual footwear, while the creep test results indicated an effective crosslinking of the adhesive. These results confirm the ability of the MCs to release IPDI during the adhesion process and act as crosslinkers for new adhesive formulations.