Multiphase flow through fractures has great significance in subsurface energy recovery and gas storage applications. Different fracture and flow properties affect flow through a fracture which is difficult to control in laboratory experiments. Here, we perform lattice Boltzmann simulations in an ensemble of synthetically generated fractures. Drainage simulations are performed at different capillary numbers, wettability, and viscosity ratios. We track the invading front and quantify breakthrough saturations and show that roughness and wettability have a profound effect on fluid invasion through a complex fracture. Invading a more viscous fluid results in more stable displacement regardless of the capillary number while at very low capillary numbers, fluid migration is dependent on the inherent structure of the fracture. Through a systematic investigation, we develop fluid displacement phase diagrams across multiple fractures, and demonstrate the importance of natural fracture features of roughness and wettability in establishing stable versus unstable displacement during multiphase flow.