Microwave drilling is a machining process that utilizes microwave energy for removing the target material through ablation. In the present work, simulation and experimental studies were carried out to understand the effect of process parameters such as input power, dielectric medium, and dielectric flowrate on the heat-affected zone (HAZ), diametrical overcut (OC), and thermal stresses developed in the borosilicate glass workpieces during microwave drilling. Sub-millimeter holes were produced in workpieces at 2.45 GHz using a graphite tool in air and transformer oil with static (immersion depth = 45 mm) and dynamic conditions (flowrate: 16, 79, 141, and 204 cm3/s). Results indicate that a decrease in input power enhances the HAZ while drilling in air and static dielectric, whereas HAZ decreases (approximately 44% and 24%) in dynamic dielectric than air and static dielectric, respectively, due to better heat dissipation and flushing of debris. Machining time was minimum while drilling with static dielectric; however, it increased with the increase in dielectric flowrate and a decrease in input power. On the other hand, overcut increased at higher input powers and lower dielectric flowrates due to enhanced ablation and heat accumulation in the machining zone. Higher thermal stresses generated in borosilicate glass while drilling in air and static dielectric, whereas flowing dielectric produced lower thermal stresses. The study determines an optimum combination of flowrate (204 cm3/s) and input power (70 W) for minimum HAZ, overcut, and thermal stresses during microwave drilling.