Polymer-based materials hold promise as low-cost, flexible efficient photovoltaic devices. Most laboratory efforts to achieve high performance devices have used devices prepared by spin coating, a process that is not amenable to large-scale fabrication. This mismatch in device fabrication makes it difficult to translate quantitative results obtained in the laboratory to the commercial level, making optimization difficult. Using a mini-slot die coater, this mismatch can be resolved by translating the commercial process to the laboratory and characterizing the structure formation in the active layer of the device in real time and in situ as films are coated onto a substrate. The evolution of the morphology was characterized under different conditions, allowing us to propose a mechanism by which the structures form and grow. This mini-slot die coater offers a simple, convenient, material efficient route by which the morphology in the active layer can be optimized under industrially relevant conditions. The goal of this protocol is to show experimental details of how a solar cell device is fabricated using a mini-slot die coater and technical details of running in situ structure characterization using the mini-slot die coater.