Mesoscale Convective Systems (MCSs), with length scales of 100 to 1000 km or more, fall into the "grey zone" of global models with grid spacings of 10s of km. Their under-resolved nature leads to model deficiencies in representing MCS latent heating, whose vertical structure critically shapes large-scale circulations. To address this challenge, we use analysis increments—the corrections applied by Data Assimilation (DA) to the model's prior state—from a 10 km Met Office operational forecast model to inform the development of a stochastic parameterization for MCS latent heating. To focus on errors in MCS feedback rather than errors due to a missing MCS, we select analysis increments from 1037 MCS tracks that the model successfully captures at the start of the DA cycle.A Machine Learning–based Gaussian Mixture Model reveals that the vertical structure of temperature analysis increments is probabilistically linked to the atmospheric environment. Bottom-heavy heating increments tend to occur in low Total Column Water Vapor (TCWV) conditions, suggesting that the model underestimates low-level convective heating in relatively dry environments. In contrast, top-heavy heating increments are linked to a moist layer overturning structure—characterized by high TCWV and strong vertical wind shear—indicating model underestimation of upper-level condensate detrainment in such environments. This probabilistic relationship is implemented in the Met Office operational forecast model as part of the MCS: PRIME stochastic scheme, which corrects MCS-related uncertainties during model integration. By enhancing top-heavy heating, the scheme backscatters kinetic energy from the mesoscale to larger scales, improving predictions of Indian seasonal rainfall and the Madden–Julian Oscillation (MJO). Future work will assess its impact on forecast busts and its potential to extend predictability.