The integration of antimicrobial peptides (AMPs) into microstructured delivery systems enhances the controlled release and stability of bioactives like Resveratrol. This study examines third-generation microparticles based on alginate and pectin with aggregated AMPs for dual antioxidant and antimicrobial effects. The AMP self-assembled into nanoparticles before forming microparticles via spray drying, improving structural stability. In silico modeling and in vitro release studies under simulated gastrointestinal conditions showed that AMP-containing microparticles provided a slower, sustained Resveratrol release compared to peptide-free systems. The Weibull model best described the release, indicating a multi-phase behavior driven by diffusion and erosion. In gastric conditions, AMP-incorporated matrices improved structural integrity, reducing release, while in intestinal conditions, partial erosion enabled controlled release. In vivo infection studies using Galleria mellonella demonstrated significant reductions in inflammation and bacterial load 48 h post-infection. These results suggest that alginate-pectin microparticles with aggregated AMPs enhance antioxidant release and maintain antimicrobial activity, making them promising for gastrointestinal applications. Further optimization will focus on maximizing localized therapeutic efficacy.