Microwave drilling is a newly developed machining technique which has demonstrated capability to deliver a cost-effective and time-efficient solution for drilling composite materials. In the current study, banana fiber reinforced composite laminates of 4 mm thickness were drilled in 4–6 seconds using microwave energy. Effects of input microwave power and fiber concentration on Heat Affected Zone (HAZ), overcut, and Material Removal Rate (MRR) were experimentally investigated. Electric field distribution at the concentrator’s tip and its circumference with respect to power and fiber fraction was studied using finite element analysis. Minimum heat affected zones of 0.9 mm2 and 1.2 mm2 were observed in cases of composites with 10% and 20% fibre fractions, respectively, at input power 810 W. Material removal rate was found to decrease with the increase in loading of fibre in the composite. Overcut was found to increase with increase in input power and volume fraction of fiber. Microscopic images revealed absence of defects like protrusions, delamination, fiber pull-outs and presence of defect like porosity. Cross-sectional SEM micrographs revealed smooth hole surfaces with insignificant taper.