Rural clinics in Nigeria often face challenges in delivering consistent quality healthcare due to limited resources and infrastructure. The study employed a mixed-methods approach including surveys, observational data collection, and multilevel regression models to analyse system performance at both individual and organisational levels. Multilevel regression revealed that the presence of adequate training for healthcare providers significantly improved patient recovery rates by 15% (95% CI: [7%, 23%]) in clinics with improved systems compared to those without. The findings suggest a need for enhanced training programmes and resource allocation strategies to optimise rural clinic performance and enhance clinical outcomes. Policy recommendations include the implementation of continuous professional development initiatives for healthcare staff and increased investment in infrastructure improvements. Treatment effect was estimated with $\text{logit}(p_i)=\beta_0+\beta^\top X_i$, and uncertainty reported using confidence-interval based inference.