Polyurea/polyurethane (PUa/PU) shell microcapsules (MCs), containing high loadings of isophorone diisocyanate (IPDI) in the core, were developed to enable the production of mono-component, eco-friendly and safer adhesive formulations for the footwear industry. IPDI microencapsulation was obtained via oil–in–water (O/W) microemulsion combined with interfacial polymerization. A methylene diphenyl diisocyanate (MDI) compound (a commercial blend of monomeric and polymeric species), with higher reactivity than IPDI and low viscosity, was added to the O phase to competitively contribute to the shell formation, improving its quality. Four different active H sources were tested, aimed at achieving a high encapsulation yield. The successful encapsulation of IPDI was confirmed by Fourier transformed infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA), while the MCs’ morphology and size distribution were assessed by scanning electron microscopy (SEM). The incorporation of a multifunctional isocyanate silane in the O phase, as “latent” active H source, led to the formation of impermeable PUa/PU-silica hybrid shell MCs with more than 60 wt.% of pure encapsulated IPDI. A proof-of-concept study shows high peeling strength and a structural type of failure of the adhesive joint, revealing an effective IPDI release. These new engineered MCs are found to be promising crosslinkers for mono-component adhesives for high demanding applications.