The antibacterial activity against Staphylococcus aureus of aerogels fabricated from colloidal suspensions of chitosan/chondroitin sulfate nanocomplexes is analyzed. Upon freeze-drying the colloidal suspensions, the aerogels presented a porous structure made of microsheets and microfibers. The aerogels could, in addition, be loaded with antimicrobial agents. Loaded with the antibiotic erythromycin, the aerogels showed crystalline deposits, affecting the topography of the samples as well as their mechanical properties, showing a decrease on the apparent Young’s modulus and hardness at 40% deformation. Loaded with elephant garlic (Allium ampeloprasum L. var. ampeloprasum) extract, the aerogels showed texturization of the microsheets and microfibers, and the higher relative mass allowed an increase on the apparent Young’s modulus and hardness at 40% deformation with respect to pristine aerogels. Unloaded aerogels showed activity against Staphylococcus aureus, including a methicillin-resistant strain. The release of erythromycin from the aerogels to an agar environment is governed by equilibrium forces with the polysaccharides, which allow modulating the load of antibiotic and its concomitant diffusion from the material. The diffusion of the active components of the elephant garlic extract did not show a dependence on the polysaccharide content, revealing a week interaction. The elephant garlic extract resulted active against the methicillin-resistant Staphylococcus aureus strain, while resistance was found for the antibiotic, revealing the therapeutic potential of the natural extract. The antimicrobial aerogels may be used for several therapeutic purposes, such as healing of infected chronic wounds.