Abstract Production of bioethanol from lignocellulosic biomass is very challenging due to the heterogenous nature of the feedstock. An efficient pretreatment is necessary for maximizing the enzymatic hydrolysis efficiency and this in turn helps in reducing the total process economy. Conventional pretreatment using acid or alkali at high temperature and pressure is limited due to its high energy input. So there is a need for alternative heating techniques which not only reduce the energy input, but increases the total process efficiency. Microwave pretreatment may be a good alternative as it can reduce the pretreatment time at higher temperature. In the present study, a comparison of three types of microwave pretreatment such as microwave-acid, microwave-alkali and combined microwave-alkali-acid were tried using sugarcane bagasse as the lignocellulosic biomass. The enzymatic saccharification efficiency and lignin removal in each pretreatment method has been evaluated. Microwave treatment of sugarcane bagasse with 1% NaOH at 600 W for 4 min followed by enzymatic hydrolysis gave reducing sugar yield of 0.665 g/g dry biomass, while combined microwave-alkali-acid treatment with 1% NaOH followed by 1% sulfuric acid, the reducing sugar yield increased to 0.83 g/g dry biomass. Microwave-alkali treatment at 450 W for 5 min resulted almost 90% of lignin removal from the bagasse. The effect of pretreatment has been also evaluated by XRD, SEM and FTIR analysis. It was found that combined microwave-alkali-acid treatment for short duration enhanced the fermentable sugar yield.