The integrity of machined holes depends on many parameters, some of which are related to the cutting tool (geometry, coating, material). Other influential parameters are related to the machining process variables (spindle speed, feed rate, workpiece material), all of which can affect the quality of the hole and drilling induced damage on its surface. This study investigates the effect of uncoated tools and four types of tool coatings (TiN-, TiCN-, TiAlN-, and TiSiN) on the hole quality and its microstructure. The study analyzed several hole geometrical metrics, namely hole size, circularity, cylindricity, and perpendicularity of an Al2024 aluminum alloy using a multi-spindle drilling process that utilizes three drills capable of creating multiple holes simultaneously. The results showed that the uncoated carbide drill gave a high-hole quality at low spindle speed. Regarding the coated drills, TiCN coated drills produced holes with the least deviation, circularity, cylindricity and perpendicularity at high spindle speeds. TiSiN–carbide coated drills produced the most oversized holes and noticeable damage and deformations on their surface following TiAlN and TiN. The common surface damage found on the inner hole surface was smearing, feed marks, and metal debris adhesion. The ANOVA results revealed that the tool type had the highest percentage contribution that mainly affected the hole quality.