This paper addresses the challenges in computing the column moist static energy (MSE) budget in climate models. Residuals from such computations often match other major budget terms in magnitude, obscuring their contributions. This study introduces a methodology for accurately computing the column MSE budget in climate models, demonstrated using the GISS ModelE3. Multiple factors leading to significant residuals are identified, with the failure of the continuous calculus’s chain rule upon discretization being the most critical. This failure causes the potential temperature equation to diverge from the enthalpy equation in discretized models. Consequently, in models using potential temperature as a prognostic variable, the MSE budget equation is fundamentally not upheld, requiring a tailored strategy to close the budget. This study introduces the “process increment method’ for accurately computing the column MSE flux divergence. This method calculates the difference in the sum of column internal energy, geopotential, and latent heats before and after applying the dynamics scheme. Furthermore, the calculated column flux divergence is decomposed into its advective components. These computations enable precise MSE budget analysis. The most crucial finding is that vertical interpolation into pressure coordinates can introduce errors substantial enough to reverse the sign of vertical MSE advection in the warm pool regions. In ModelE3, accurately computed values show MSE import via vertical circulations, while values in pressure coordinates indicate export. This discrepancy may prompt a reevaluation of vertical advection as an exporting mechanism and underscores the importance of precise MSE budget calculations.