Drilling is one of the most performed machining operations for riveting and assembly operations in many industrial sectors. The accuracy of the drilled holes and their surface finish play a vital role in the longevity and performance of the machined components, which, in turn, increase productivity. Therefore, this study investigated the effect of the multi-spindle drilling process on dimensional hole tolerances, such as hole size, circularity, cylindricity, and perpendicularity. In addition, the surface defects formed in the holes were examined using scanning electron microscopy. Three aluminium alloys, AA2024, AA6061, and AA5083, which are commonly used in the aerospace, automotive, and marine sectors, were chosen as the study materials. The results showed that the holes drilled in AA2024 gave less circularity error, cylindricity error, and perpendicularity error. In the case of hole size, the holes drilled in AA6061 were less deviated from the nominal size following holes drilled in AA2024 and AA5083 alloys. Surface damage in the form of metal debris adhesion, smeared material, side flow, and feed marks was found on the inner hole surface. Holes drilled in AA5083 alloy had the worst surface finish and were the most oversized, which was associated with noticeable damage and deformations in their inner surface. The ANOVA results revealed that the spindle speed was more influential than feed and mainly affected the hole size and cylindricity errors. However, in the case of circularity error and perpendicularity error, drilling parameters were found to be insignificant.