Biopolymer-based aerogels can be obtained by supercritical drying of wet gels and endowed with outstanding properties for biomedical applications. Namely, polysaccharide-based aerogels in the form of microparticles are of special interest for wound treatment and can also be loaded with bioactive agents to improve the healing process. However, the production of the precursor gel may be limited by the viscosity of the polysaccharide initial solution. The jet cutting technique is regarded as a suitable processing technique to overcome this problem. In this work, the technological combination of jet cutting and supercritical drying of gels was assessed to produce chitosan aerogel microparticles loaded with vancomycin HCl (antimicrobial agent) for wound healing purposes. The resulting aerogel formulation was evaluated in terms of morphology, textural properties, drug loading, and release profile. Aerogels were also tested for wound application in terms of exudate sorption capacity, antimicrobial activity, hemocompatibility, and cytocompatibility. Overall, the microparticles had excellent textural properties, absorbed high amounts of exudate, and controlled the release of vancomycin HCl, providing sustained antimicrobial activity.