The present work focused on solvent-free microwave-assisted esterification (MAE) of isoamyl acetate. It is based on the hypothesis that isoamyl acetate yield can be affected by variables such as different acyl donors (acetic acid, acetic anhydride, and ethyl acetate), lipases (Novozyme 435 and Lipozyme RMIM) and microwave power levels (100 and 200 W). Furthermore, this study aimed to make comparisons between MAE and other esterification techniques, namely the ohmic, ultrasound, and incubator. Maximum isoamyl acetate yield (100%) was obtained at a power level of 100 W in MAE after 1 h when acetic anhydride and Novozyme 435 were used in the process. MAE had the lowest specific CO2 emission (16 g/g isoamyl acetate) and specific electric energy consumption (0.02 kWh/g isoamyl acetate) in comparison with other esterification techniques. The MAE had no adverse effects on the structure of Novozyme 435 beads according to scanning electron microscopy images. After using the same Novozyme 435 repeatedly for 7 times, the yield of isoamyl acetate became lower than 19%. In conclusion, MAE can be proposed as a green technique for the lipase esterification of different flavoring esters.