Nanoparticles (NPs), offering high specific surface, are considered as the best potential anti-microbial agents for a wide range of medical nanotechnology. Among them, silver NPs (AgNPs) allow high biocidal activity. A design of ecological capsules is proposed where AgNPs of 22 nm in diameter are grafted on the surface of biobased nanocrystals obtained from cellulose (CNC) and chitin (ChiNC). These silver nanohybrids are dispersed in calcium-alginate microgels of 45–50 μm in diameter using microfluidic tools. Such double level of immobilization of AgNPs leads to highly stable carriers, prolongs shelf life and raises bioactivity, with a precise control of well dispersed AgNPs as determined by scanning transmission electron microscopy, UV-Vis spectroscopy and atomic absorption spectroscopy. Preliminary tests for antimicrobial activities of these new microgels have shown a significant inhibitory effect on Candida albicans, the most common fungal pathogen, responsible for thrush and vaginal yeast infections, for very low levels of silver.