Chitosan/xanthan gum microcontainers with a core-shell structure formed due to chemical interactions between polysaccharide chains induced by ultrasonication are presented. Containers were prepared by sonication of water-immiscible (oil-like) liquids in the solution of polysaccharides. One-step fabrication of the container permanent shell is possible, because of the contribution of ultrasonically caused formation of hydrogen bonds and amide linkages. We synthesized containers in a wide size range from 350 nm to 7500 nm, varying in oil/water ratio. The microcontainers were modified with oppositely charged polyelectrolytes and microparticles, which could be used to impart the specified properties to the system. The biocide 4,5-dichloro-2-n-octyl-4-isothiazoline-3-one (DCOIT) was loaded into the proposed containers by utilizing its solution as an oil phase. The following incorporation of the DCOIT containers into the polymer coating demonstrated more sustained antimicrobial activity (∼30%) of the biocide in the encapsulated state, compared to its non-encapsulated form.