Primary Health Care (PHC) is the main point of contact between users and the healthcare system, making the assessment of the quality and performance of its Functional Units (FUs) essential. As respiratory disease management is part of their routine activity, it is relevant to examine how organisational characteristics influence this practice.To assess how the different characteristics of each FU affect their performance in managing respiratory diseases in mainland Portugal, by analyzing several clinical governance tools available on the BI-CSP® platform: the “Global Performance Index” (IDG_IPDA), the subarea “Disease Management – Respiratory System Diseases,” and its associated indicators.A cross-sectional observational study was conducted using public data extracted from the BI-CSP® platform, covering 940 FU (USF-B and UCSP) across all Regional Health Administrations (ARS). Indicators analyzed included COPD and asthma follow-up, influenza vaccination coverage, hospitalization rates, and diagnostic proportions. Descriptive statistics, correlation analyses, multiple linear regressions, and multivariate tests (Wilks' Lambda) were applied.USF-B units, those with medical residents, and those with a higher number of physicians demonstrated better performance across the evaluated indicators. The IDG_IPDA proved to be a statistically significant predictor in nearly all models. The regions defined by the former ARS also exerted a statistically significant influence on the outcomes. Conversely, hospitalizations due to pneumonia and asthma were not explained by the organizational variables included in the analysis.Performance in respiratory disease management is associated with the organizational model, the presence of medical residents, physician staffing levels, and the regional context. Strategies aimed at strengthening the USF-B model, enhancing clinical training, and promoting regional equity may improve care outcomes. The cross-sectional nature of the data used prevents the establishment of causal relationships between the organisational characteristics of the UF and the outcomes obtained. Although statistically significant associations are identified, it is not possible to determine with certainty whether these variables were the direct cause of the variations in performance indicators.The performance of FU in the management of chronic respiratory diseases in PHC in Portugal is significantly associated with several organisational characteristics, such as pay-for-performance schemes, which may influence priorities in terms of public investment.