The dynamic development of various branches of medicine and pharmacy, along with the emergence of new preventive and alternative therapies for various diseases, creates opportunities for new solutions utilizing carriers of active substances. Their therapeutic effect may occur through direct contact with skin lesions or indirectly, where medicinal substances penetrate the capillary network in the deeper layers of the skin and reach the bloodstream. The aim of the research was to obtain carriers with a matrix consisting of two renewable-source polymers (chitosan and ethylcellulose) and a core material derived from Ginkgo biloba green leaf extract (GBE). The obtained ethylcellulose microcapsules with encapsulated chitosan nanoparticles with extract {Et[Ch(GB)NP]} were characterized with respect to size, shape, surface morphology (SEM microscopy), and active substance release kinetics (UV-VIS and mathematical release models). The kinetics of active substance release were analyzed using UV-VIS spectroscopy and mathematical release models. The released active components were assessed microbiologically for activity against six bacterial strains and two fungal strains, as well as chromatographically using HPLC-ESI-QTOF-MS/MS fingerprinting. The microcapsules with a dual polymer layer exhibited a slow release of the core material, which demonstrated microbiological activity. The strongest antimicrobial effects were observed against Klebsiella pneumoniae and Salmonella enteritidis, with a minimum inhibitory concentration (MIC) of 410 µg/mL. The release of the core material from the double-layer polymer structures was more efficient in a physiological saline environment, with the best fit for the extract release kinetics following a zero-order model (regression coefficient R² = 0.9939). The obtained microcapsules with a dual polymer layer show great potential for therapeutic applications in the medical industry. Their controlled release properties and antibacterial effectiveness make them a promising carrier for active substances in modern therapies.