<p>The drilling efficiency of multilayer biofiber-reinforced epoxy composites is examined by focusing on hybrid plain-woven fabric structures enhanced with nano-sized industrial waste (IW) filler. The study evaluates spindle speed, feed rate, and three tungsten carbide-coated tools (TiCrN, TiAlN and TiN) to assess hole quality based on delamination, surface roughness, and circularity error. The experimental procedures, based on Taguchi’s L9 orthogonal array, involve drilling composites reinforced with hybrid interwoven and intra-woven jute, white flax, and brown flax fibers, combined with 2% (by wt) nano-IW filler. Performance is influenced by the coating hardness and the interaction at the tool/composite interface. Delamination, surface roughness, and circularity error were evaluated based on drilling parameters. Results indicate that TiN-coated tools achieve a maximum reduction in delamination by 7.63% at the front, 9.39% at the back of the hole, and surface roughness by 47.16% for IW-filled composite. Meanwhile, TiCrN-coated tools resulted in a 26.04% reduction in circularity error for nano-filled composites. Drill tool coating was identified as the primary factor influencing hole quality, followed by spindle speed and feed rate. ANOVA and regression analyses confirmed the statistical significance and relative contribution of each parameter, highlighting the drilling conditions of the 9th trial as the most effective for enhancing hole quality with the applied coatings.</p> Graphical abstract <p></p>