Natural fiber reinforced composites are becoming popular in various industrial and commercial applications as structural components. Unlike conventional materials, machining of fiber composites is critical due to its heterogeneous structure. Hence, it is necessary to understand the machining behaviour of fiber reinforced composites. Hybrid composites reinforced with banana fiber and fly ash filler in polyester matrix were fabricated and then evaluated for drilling performance. Drilling experiments were performed using the Taguchi L27 orthogonal array. The influence of feed rate (A), cutting speed (B) and filler content (C) on thrust force, surface roughness, and delamination factor entry and exit were using Taguchi and Analysis of variance (ANOVA) techniques. The results revealed that (i) Minimum thrust for attained at filler content (A) 1 vol %, speed (B) 3000 r/min, and feed (C) 100 mm/min, (ii) Minimum surface roughness at filler content A (3 vol %), speed B (2000 r/min), and feed rate C (100 mm/min) and (iii) Minimum peel up and push out delamination at filler content (A) as, 5vol %, speed (B) 2000 r/min, and feed (C) 100 mm/min. This study provides machining insights on agro-industrial waste based polymer composites for structural applications.