Compliance with the future CO2 emission limits for the fleet of vehicles sold presents a major challenge for the automotive industry. To comply with these stringent limits, one solution is mobility using hydrogen as an energy carrier. In this context, the development of Proton Exchange Membrane (PEM) fuel cells for commercial vehicle applications, both on- and off-road, is of significant interest due to the non-existent CO2 emissions. However, performance of these devices is closely related to the control concepts that are used to ensure high efficiency, good transient performance, high reliability & durability as well as safe operation. To address these challenges, this paper presents a modular Fuel Cell Control Software which offers the potential to be used for different P&ID (Piping & Instrumentation Diagram) configurations of fuel cell systems. The presented software controls and monitors the stack and the Balance of Plant (BoP) components and communicates with the main vehicle controller. To realize this, the control software consists of a start-up and shut-down procedure that has been coordinated with various fuel cell stack manufacturers. It allows a wide range of diagnostics to check various sub-systems. The main control variables, namely temperature, pressure, humidity, and air stoichiometry, which directly affect the fuel cell performance, are identified. Depending on the system complexity, the modular software takes into account different approaches to mass flow, pressure and humidity control, e.g. using throttles and bypasses. Particular attention is paid to the optimization of the purge/drain strategy. Furthermore, the challenges due to component deviations or aging are considered in closed-loop power control. In addition to the functional correlations and the principle layout of the novel algorithms, the paper delivers also experimental results that demonstrate the merits for a reliable operation.