Community health centers in Uganda play a crucial role in providing essential healthcare services to underserved populations. However, their effectiveness and cost-effectiveness have not been thoroughly evaluated. A qualitative methodological evaluation was conducted, employing a DiD approach to analyse data from multiple sites. The analysis accounts for potential confounding variables through robust statistical methods. The difference-in-differences model revealed a significant improvement in health outcomes among the intervention group compared to controls (p < 0.05). The DiD method demonstrated its effectiveness in assessing cost-effectiveness of community health centers, providing valuable insights for policy formulation. Policy makers should prioritise investment in infrastructure and human resources at community health centers to enhance service delivery and patient outcomes. Community Health Centers, Difference-in-Differences (DiD), Cost-Effectiveness, Uganda Treatment effect was estimated with $\text{logit}(p_i)=\beta_0+\beta^\top X_i$, and uncertainty reported using confidence-interval based inference.