In this work, active alginate-based coatings were developed using hydroxyapatite nanoparticles as potential carriers for quercetin glycoside compounds. The coatings were produced through the layer-by-layer method and loaded with different concentrations of quercetin and hydroxyapatite/quercetin complexes. In-vitro release studies of the quercetin through the coatings were performed in an aqueous medium: even if the hydroxyapatite nanocrystals slow down the diffusion process, quercetin released reached the equilibrium in one day for all coatings. Lastly, antimicrobial tests show that all active coatings display antibacterial activity against Pseudomonas fluorescens. This study highlights the real possibility of applying active edible coating loaded with hydroxyapatite/quercetin complexes to the food shelf life extension.