The present research work explores the consequence of eco-friendly sodium bicarbonate treatment on drilling behavior of jute fiber reinforced polyester composites. The fiber surface treatment was done by immersing the jute fibers in sodium bicarbonate solution (10 wt.%) for five days at room temperature. The raw and treated jute fiber composites were produced through compression molding process. The drilling behavior was expressed in terms of delamination factor (at entry and exit) and surface finish. The response surface methodology coupled with three factors—three levels Box–Behnken Design was used to study the interactive effects of process variables (drill diameter, feed, and cutting speed) on delamination factor and surface finish. Furthermore, the significance of the developed model was examined through analysis of variance. The chip morphology of the fabricated composites was examined to assess the quality of the drilled hole. The fractography analysis of the machined surface has also been carried using scanning electron microscopy. The outcomes revealed that the sodium bicarbonate treatment of jute fiber improved the machinability of the composites.