The encapsulation of active components is currently used as common methodology for the insertion of additional functions like self-healing properties on a polymeric matrix. Among the different approaches, polyurea microcapsules are used in different applications. The design of polyurea microcapsules (MCs) containing active diisocyanate compounds, namely isophorone diisocyanate (IPDI) or hexamethylene diisocyanate (HDI), is explored in the present work. The polyurea shell of MCs is formed through the interfacial polymerization of oil-in-water emulsions between the highly active methylene diphenyl diisocyanate (MDI) and diethylenetriamine (DETA), while the cores of MCs contain, apart from IPDI or HDI, a liquid Novolac resin. The hydroxyl functionalities of the resin were either unprotected (Novolac resin), partially protected (Benzyl Novolac resin) or fully protected (Acetyl Novolac resin). It has been found that the formation of MCs is controlled by the MDI/DETA ratio, while the shape and size of MCs depends on the homogenization rate applied for emulsification. The encapsulated active compound, as determined through the titration of isocyanate (NCO) groups, was found to decrease with the hydroxyl functionality content of the Novolac resin used, indicating a reaction between NCO and the hydroxyl groups. Through the thorough investigation of the organic phase, the rapid reaction (within a few minutes) of MDI with the unprotected Novolac resin was revealed, while a gradual decrease in the NCO groups (within two months) has been observed through the evolution of the Attenuated Total Reflectance—Fourier-Transform Infrared (ATR-FTIR) spectroscopy and titration, due to the reaction of these groups with the hydroxyl functionalities of unprotected and partially protected Novolac resin. Over longer times (above two months), the reaction of the remaining NCO groups with humidity was evidenced, especially when the fully protected Acetyl Novolac resin was used. HDI was found to be more susceptible to reactions, as compared with IPDI.