Isocyanate-filled microcapsules are gaining increased attention for their role in developing self-healing materials, thereby reducing maintenance costs and increasing polymer durability. Nevertheless, microencapsulating highly reactive -NCO groups remains a challenging task in the literature. Likewise, considerable efforts have been directed towards developing polymers from renewable and biobased sources, which could also be applied to microcapsule synthesis. In this work, lignin, an abundant biopolymer, was used as a solid stabilizer for oil-in-water (O/W) interfaces, enabling the encapsulation of highly reactive isocyanate. Hybrid polyurethane/polyurea microcapsules containing reactive methylenediphenyl diisocyanate (MDI) were obtained via optimized O/W Pickering emulsions using lignin for system stabilization. This optimized process facilitated shell formation via the reaction of diisocyanate with lignin and water, eliminating the need for additional chain extenders. Scanning electron microscopy revealed the formation of spherical and rough microcapsules, while infrared spectroscopy confirmed the presence of residual free -NCO groups, indicating effective encapsulation of MDI. Additionally, a core -NCO concentration of 11 wt% was confirmed by titration. The microcapsules were further assessed as components in self-healing epoxy coatings. Their incorporation resulted in the retardation of corrosion on a low carbon steel panel after 72 h of submersion in a saline solution. Electrochemical impedance spectroscopy (EIS) confirmed a significant increase of approximated 620% in impedance modulus after 83 days of immersion in a 3.5 wt% NaCl solution, compared to the neat epoxy coating. These findings suggest a promising technological application of this material for the advancement of self-healing epoxy-based coatings and composites.