Recent studies in Uganda have shown mixed results regarding efficiency gains in manufacturing systems. However, these studies often lack robust methodological frameworks to accurately measure and analyse such gains. The DiD model will be employed to analyse changes in manufacturing plant performance before and after certain interventions, such as policy reforms or technological upgrades. This approach allows us to isolate the effect of these interventions from other potential confounders. This theoretical framework lays out a robust methodology for future empirical studies on manufacturing system efficiency in Uganda and beyond. Future researchers should consider the DiD model as a foundational tool to assess and report efficiency gains in manufacturing systems, ensuring transparent and replicable results. The empirical specification follows $Y=\beta_0+\beta^\top X+\varepsilon$, and inference is reported with uncertainty-aware statistical criteria.