In this work we study the effect of metachronal waves on the flow created by magnetically driven plate-like artificial cilia in microchannels using numerical simulations. The simulations are performed using a coupled magneto-mechanical solid–fluid computational model that captures the physical interactions between the fluid flow, ciliary deformation and applied magnetic field. When a rotating magnetic field is applied to super-paramagnetic artificial cilia, they mimic the asymmetric motion of natural cilia, consisting of an effective and recovery stroke. When a phase difference is prescribed between neighbouring cilia, metachronal waves develop. Due to the discrete nature of the cilia, the metachronal waves change direction when the phase difference becomes sufficiently large, resulting in antiplectic as well as symplectic metachrony. We show that the fluid flow created by the artificial cilia is significantly enhanced in the presence of metachronal waves and that the fluid flow becomes unidirectional. Antiplectic metachrony is observed to lead to a considerable enhancement in flow compared to symplectic metachrony, when the cilia spacing is small. Obstruction of flow in the direction of the effective stroke for the case of symplectic metachrony was found to be the key mechanism that governs this effect.