Abstract Understanding controls on Mesoscale Convective Systems (MCSs) is critical for predicting rainfall extremes across scales. Spatial variability of soil moisture (SM) presents such a control, with ∼ ${\sim} $200 km dry patches in the Sahel observed to intensify mature MCSs. Here we test MCS sensitivity to spatial scales of surface heterogeneity using a framework of 78 Unified Model experiments initialized from scale‐filtered SM. We demonstrate the control of SM heterogeneity on MCS populations, and the mechanistic chain via which spatial variability propagates through surface fluxes to convective boundary layer development and storm environments. When all sub‐synoptic SM variability is homogenized, peak MCS counts drop by 23%, whereas maintaining small‐scale variability maintains primary initiation rates, reducing the drop in MCS totals. In sensitivity experiments, boundary layer development prior to MCSs is similar to that over mesoscale dry SM anomalies, but driven by cloud‐free slots of increased shortwave radiation. This reduces storm numbers and potential predictability.