We report on the stabilization of an oil-in-water (O/W) emulsion to, combined with interfacial polymerization, produce core–shell polyurea microcapsules (MCs) containing isophorone diisocyanate (IPDI). These will act as crosslinkers for mono-component adhesives. The emulsion stabilization was evaluated using three types of stabilizers, a polysaccharide (gum arabic) emulsifier, a silicone surfactant (Dabco®DC193), a rheology modifier (polyvinyl alcohol), and their combinations. Emulsion sedimentation studies, optical microscopy observation, and scanning electron microscopy enabled us to assess the emulsions stability and droplet size distribution and correlate them to the MCs morphology. Fourier transform infrared spectroscopy and thermogravimetric analysis revealed the MCs composition and enabled us to evaluate the encapsulation yield. All stabilizers, except DC193, led to spherical, loose, and core–shelled MCs. The rheology modifier, which increases the continuous phase viscosity, reduces the emulsion droplets sedimentation, keeping their size constant during the MCs’ synthesis. This allowed us to obtain good quality MCs, with a smaller average diameter, of approximately 40.9 µm mode, a narrower size distribution and 46 wt% of encapsulated IPDI. We show the importance of the emulsion stability to tune the MCs morphology, size, and size distribution, which are critical for improved homogeneity and performance when used, e.g., in natural and synthetic adhesive formulations industry.