New promising manganese-containing nanobiocomposites (NCs) based on natural polysaccharides, arabinogalactan (AG), arabinogalactan sulfate (AGS), and κ-carrageenan (κ-CG) were studied to develop novel multi-purpose trophic low-dose organomineral fertilizers. The general toxicological effects of manganese (Mn) on the vegetation of potatoes (Solanum tuberosum L.) was evaluated in this study. The essential physicochemical properties of this trace element in plant tissues, such as its elemental analysis and its spectroscopic parameters in electron paramagnetic resonance (EPR), were determined. Potato plants grown in an NC-containing medium demonstrated better biometric parameters than in the control medium, and no Mn accumulated in plant tissues. In addition, the synthesized NCs demonstrated a pronounced antibacterial effect against the phytopathogenic bacterium Clavibacter sepedonicus (Cms) and were proved to be safe for natural soil microflora.