Finite element analysis (FEA) on conventional drilling of two bio-composite materials, consist of hybrid woven flax-basalt and woven basalt fibre with vinyl ester matrix, designated as composite materials A and B respectively, has been conducted. The simulation results using LS-DYNA and ANSYS software depict that different reinforcements (flax and basalt fibres) of the composite materials significantly influenced the degree of resistance, strength, deformation and elasticity exhibited during the machining process. It was observed that drilling-induced damage were experienced in different degrees by the materials. The quality of the holes produced was affected by the characteristics of these materials, when experimentally validated. Also, significant differences in tensile strength and impact of the drilling operation on the plies of the two materials were observed. Material A experienced higher stress and lower tensile strength, resulting into a higher level of push-out delamination, uncut-fibre and fibre pull-out, among other rampant drilling-induced damage, than material B. Both materials possessed high stress and deformation, which were more at the edges (entry and exit) of the drilled holes rather than the centre point where the drill impacted the hole. The equivalent elastic strain further shows a high level of impact at the surface of material A, unlike material B. Comparatively, the composite material B (woven basalt fibre reinforced polymer) has a better machinability when compared with hybrid material A (woven flax-basalt). Hence, it implies that the FRP composite materials responded to damage differently under same machining (drilling) process and condition.