The credibility of regional climate simulations over West Africa stands and falls with the ability to reproduce the West African monsoon (WAM) whose precipitation plays a pivotal role for people’s livelihood. In this study, we simulate the WAM for the wet year 1999 with a 27-member multi-physics ensemble of the Weather Research and Forecasting (WRF) model. We investigate the inter-member differences in a process-based manner in order to extract generalizable information on the behavior of the tested cumulus (CU), microphysics (MP), and planetary boundary layer (PBL) schemes. Precipitation, temperature and atmospheric dynamics are analyzed in comparison to the Tropical Rainfall Measuring Mission (TRMM) rainfall estimates, the Global Precipitation Climatology Centre (GPCC) gridded gauge-analysis, the Global Historical Climatology Network (GHCN) gridded temperature product and the forcing data (ERA-Interim) to explore interdependencies of processes leading to a certain WAM regime. We find that MP and PBL schemes contribute most to the ensemble spread (147 mm month−1) for monsoon precipitation over the study region. Furthermore, PBL schemes have a strong influence on the movement of the WAM rainband because of their impact on the cloud fraction, that ranges from 8 to 20 % at 600 hPa during August. More low- and mid-level clouds result in less incoming radiation and a weaker monsoon. Ultimately, we identify the differing intensities of the moist Hadley-type meridional circulation that connects the monsoon winds to the Tropical Easterly Jet as the main source for inter-member differences. The ensemble spread of Sahel precipitation and associated dynamics for August 1999 is comparable to the observed inter-annual spread (1979–2010) between dry and wet years, emphasizing the strong potential impact of regional processes and the need for a careful selection of model parameterizations.