Urban primary care networks are a critical component of health systems in rapidly urbanising African nations, yet robust methodological frameworks for evaluating their clinical performance are lacking. This study aimed to methodologically evaluate the structure and effectiveness of urban primary care networks by developing and applying a multilevel model to analyse clinical outcomes across networked facilities. We conducted a retrospective cohort analysis using routine health information system data from multiple urban networks. A three-level random intercepts model was specified: $y_{ijk} = \beta_0 + \beta X_{ijk} + u_{k} + v_{jk} + e_{ijk}$, where $u_{k}$ and $v_{jk}$ are random effects for network and facility, respectively. Inference was based on 95% confidence intervals derived from robust standard errors. Network-level factors explained a significant 18% of the variance in composite chronic disease control outcomes. Facilities with integrated pharmacy services within their network demonstrated a 12.4 percentage point improvement in hypertension control (95% CI: 8.1 to 16.7) compared to those without. The methodological approach confirms that urban primary care networks exert a measurable, significant influence on clinical outcomes, with structural integration being a key modifiable factor. Health policy should prioritise the standardised measurement of network-level characteristics and invest in cross-facility service integration, particularly clinical support functions, to improve population health outcomes. primary health care, health systems research, multilevel analysis, health services evaluation, urban health, Ethiopia This paper provides a novel methodological framework for quantifying the specific contribution of network structure to clinical performance, moving beyond facility-level assessment.