Nickel-based superalloys have superior strength properties at higher temperature ranges and thus have become increasingly important in manufacturing gas turbine components for aerospace industry. However, the desire for a larger thrust-weight ratio has raised the typical operating temperature in a gas turbine; thus, thermal barrier coatings are essential. The present work compares the micro-drilling performance of ceramic-coated Nimonic 90 nickel superalloy under dry, flood and 0.5% graphene-based NMQL conditions. The biodegradable acid oil was used as a base oil, and the assessment comprised surface integrity in terms of surface roughness inside the hole and micro-crack formation and hole quality based on the diametrical overcut and taper ratio. Spindle speed (1000, 2000 and 3000 rpm) and feed rate (3, 6, and 9 μm/rev) were changed in three levels, and Taguchi L9 array was applied for the design and analysis of the experiments. Ti-Al-N coated tungsten carbide drill of diameter 700 μm was used, and Analysis of variance (ANOVA) revealed that spindle speed was the utmost important parameter impacting surface roughness, while speed and feed rate both influenced overcut and taper ratio. 0.5% Graphene-based NMQL lubrication condition significantly diminished the surface roughness by 52.67%, overcut by 46.86% and the taper ratio by 48.87% as compared to dry condition. Furthermore, in the NMQL condition, micro-crack development and ceramic layer damage were minimized, resulting in better surface integrity. In addition, burr development was minimized at the hole periphery, and tool wandering was not seen in the NMQL condition. Hence the hole quality was superior in NMQL conditions as compared to the dry and flood lubrication.