The study describes chemo-enzymatic synthesis of organic disulphide compounds. The reaction was initiated by hydrolysis of thiol acetates using hydrolytic enzyme lipase (PPL) immobilized on to magnetic nanoparticles and subsequent formation of organic disulphide compounds. Lipase was immobilized on to the magnetic nanoparticles by co-precipitation method via epichlorohydrin chitosan cross-linking, under mild and eco-friendly conditions. The immobilized lipase enzyme exhibited broad range of substrate specificity in synthesizing disulphide compounds, which involves both intra and inter-molecular disulphide bond formation under anaerobic conditions. The disulphide compounds synthesized also show a promising antimicrobial activity.