Chitin is an abundant natural polymer and its deacetylated derivative chitosan has been a focus for the development of biobased, biocompatible and antimicrobial materials. In this work, a green and scalable route to grafting polycaprolactone (PCL) to chitosan using an enzyme catalysed reactive extrusion process is described. FTIR, 1H and 13C NMR spectroscopy and HSQC analysis confirm grafting of PCL to chitosan and show differences in the grafting pattern obtained using two commercially produced lipase enzymes from Candida antarctica (CALB® and NovoCor®). The thermostable NovoCor enzyme gave a much higher grafting yield (96.3%) than the less thermostable CALB enzyme (5.90%). In the esterification reaction, CALB preferentially catalyses reaction on primary OH groups at the C-6 position of chitosan, whereas NovoCor catalyses on the secondary OH groups of chitosan at the C-3 position. This is related to the differences in the selectivity of the two lipase enzymes. The control synthesized without enzyme did not show any grafting reaction. The degree of crystallinity and thermal stability of the lipase catalysed copolymer was reduced compared to unmodified chitosan. Moreover, the PCL grafted chitosan produced by a solvent free reactive extrusion route retained antimicrobial property against E.coli. Such grafted co-polymers may have applications in the controlled release coatings and tissue culture surfaces.