Self-healing anticorrosion composite coatings containing isophorone diisocyanate-loaded polyurethane microcapsules were developed, and comprehensive research on prepolymer and microcapsules synthesis, as well as functional composite coatings preparation and characterization, was performed. The influence of the prepolymer type and the concentration of the stabilizing agent used in the synthesis procedure on the properties of the microcapsules was studied in detail. For this purpose, three different prepolymers were prepared from toluene-2,4-diisocyanate (TDI) and either glycerol, 1,4-butanediol, or 1,6-hexanediol, and their chemical properties were investigated. Microcapsules were synthesized from the obtained prepolymers, according to the oil-in-water polymerization method, where 1,6-hexanediol was used as a chain extender, while the concentration of the stabilizing agent in the synthesis procedure was varied. Microcapsules prepared from TDI-glycerol prepolymer, synthesized in the presence of 10 wt% of the stabilizing agent, showed superior chemical, morphological, and thermo-gravimetrical properties; thus, they were incorporated into the coating in the concentration of 20 wt%. The prepared composite coatings demonstrated self-healing and anticorrosion properties, and thus the developed microcapsules show great potential for the incorporation into the composite anticorrosion coatings at critical points where damage can easily occur, providing longer and more efficient anticorrosion protection.