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Abstract This study investigates the role of soil moisture (SM) on the initiation and organization of convective systems using the convection‐permitting ICOsahedral Non‐hydrostatic (ICON) model. We conduct two sets of experiments: a Control experiment with interactive SM and a fixed SM experiment (FixedSM) with invariable SM conditions. We focus on two regions in South America: the Amazon and southeastern South America (SESA). Larger organized convective systems are associated with greater SM heterogeneity in both regions, though other large‐scale synoptic influences affect the robustness of this relationship in SESA. These results remain largely unaffected by disabling the effects of precipitation on SM in the FixedSM experiment, and complementary analyses using satellite‐based estimates of SM and precipitation support these findings. Spatial compositing of mesoscale environments in the Amazon shows the presence of well‐defined SM gradients, at a length scale of a few hundred kilometers, many hours before convective system detection. Larger SM gradients correspond to larger gradients in thermodynamic variables, particularly surface temperature and sensible heat flux, and are associated with larger convective systems. Overall, our findings suggest that surface heterogeneities such as SM gradients not only affect deep convection initiation, as previously suggested, but they can also encourage the growth and organization of convective systems into larger clusters, particularly in the absence of significant synoptic influences.