Natural polymer-based drug carriers have been developed for antimicrobial applications but several problems remain with their poor controllability of drug loading and degradation. We introduce a novel method to produce improved antibiotic alginate fiber with high drug entrapment properties and a delayed degradation profile. A microfluidic spinning system with a low-polarity isopropyl alcohol (IPA) sheath flow was used to dehydrate an alginate/ampicillin aqueous solution and to form densely packed fiber with enhanced drug loading efficiency. The amounts of ampicillin initially loaded in the IPA-fiber were much higher than in the conventional water-based fiber and they released a more prolonged profile. The fibers were characterized by analyzing the morphology, mass loss and structural properties. The fibers were also used for an in vivo infected wound healing study. The results showed that the IPA-based fibrous alginate drug carrier possesses superior properties for loading drugs and potentials for wound healing applications with easy management.