A 3D numerical simulation of a four-wing flapping micro-aerial vehicle (FMAV), known as the DelFly Micro, is performed using an immersed boundary method Navier–Stokes finite volume solver at Reynolds numbers of 5500. Our objective is to obtain an insight about the aerodynamics of the FMAV which uses a biplane wing configuration. Results show that compared with the flapping kinematics of the DelFly II, that of the DelFly Micro gives higher thrust at the same efficiency. We also investigate the effect of wing flexibility on the aerodynamic performance in the biplane configuration context through prescribed flexibility. Increasing the wing' spanwise flexibility increases thrust but increasing chordwise flexibility causes thrust to first increase and then decrease. Moreover, combining both spanwise and chordwise flexibility outperforms cases with only either spanwise or chordwise flexibility.