A natural sap from mature coconut palm known as coconut neera is enriched with essential minerals and vitamins. Rapid microbial fermentation affects neera processing industries because it spoils the physicochemical properties. There are various methods in preservation that extend the shelf life of coconut neera. The addition of nisin is one of the methods which protect neera against fermentation. Therefore, the study is focused to identify the effective combination of nisin (50 ppm) with preservatives like sodium benzoate (500, and 1000 ppm), and calcium carbonate (2500, and 3000 ppm) at two different combinations in neera. At the end of 21 d, 3000 ppm calcium carbonate with 50 ppm nisin in N4 treatment had an effective reduction of 120 × 10⁵ CFU/ml and 143 × 10² CFU/ml for total bacteria and total yeast count. The reduced microbial survival resulted in the pH of 10.45 ± 0.05, total soluble solids of 15.43 ± 0.12 °Brix, and total acidity of 1.11 ± 0.04 mg/ L, at this combination. The treatment of nisin with 3000 ppm calcium carbonate demonstrated the high red fluorescence bacterial cells than the treatment of nisin with 1000 ppm sodium benzoate. Additionally, the microorganisms in N4 treatment precipitated 65.34% Ca²⁺ from 79.96% in XRF intensity analysis. The synergistic effect of nisin and calcium carbonate explored their antimicrobial activity against the heterogeneous microbial population in coconut neera. The concentration of 3000 ppm calcium carbonate and nisin 50 ppm preserves the physicochemical and sensory qualities, up to 21 d at 4°C, and offer hope for the industrial-scale implementation.