The search for effective and eco-friendly alternatives to conventional antibiotics is essential due to the global threat of antimicrobial resistance. In this study, selenium nanoparticles (Se-NPs) were biosynthesized using an aqueous rhizome extract of Alpinia officinarum Hance (AOE; lesser galangal) as a natural reducing and stabilizing agent. Chitosan (Cht), extracted from Fenneropenaeus indicus with a deacetylation degree of 91.4%, was converted into nanochitosan (NCht) with an average diameter of 60.71 nm and a surface charge of + 39.2 mV. The AOE-mediated Se-NPs were spherical, with an average size of 34.6 nm and a surface charge of –23.32 mV. Dynamic light scattering (DLS), zeta potential analysis, transmission and scanning electron microscopy (TEM, SEM), ultraviolet–visible spectroscopy (UV–Vis), and Fourier transform infrared spectroscopy (FTIR) confirmed the successful synthesis and conjugation of NCht with AOE/Se-NPs. The antibacterial activity of the nanocomposites was evaluated against Aeromonas hydrophila, Pseudomonas sp., and Staphylococcus aureus using inhibition zone diameter (IZD) and minimum inhibitory concentration (MIC) assays. NCht/AOE/Se-NPs exhibited the most potent antibacterial activity, producing the largest inhibition zones and the lowest MIC values, with S. aureus being the most resistant and A. hydrophila the most sensitive strain. SEM imaging of A. hydrophila exposed to NCht/AOE/Se-NPs revealed extensive structural damage, with complete bacterial degradation observed within 8 h. Antioxidant potential was assessed via DPPH radical scavenging, with concentrations ranging from 15.625 to 500 μg/mL. NCht/AOE/Se-NPs demonstrated the strongest activity (IC50 = 54.3 μg/mL), approaching the efficacy of ascorbic acid. These findings highlight the synergistic enhancement of antioxidant and antibacterial properties when combining NCht with AOE/Se-NPs. The developed nanocomposite offers a safe, bio-based, and environmentally sustainable approach for