There is evidence of the efficacy of collaborative health interventions with pharmacies and primary care providers but little of its real-world effectiveness. We aimed to assess the effectiveness and discuss the design and challenges of hypertension and hyperlipidemia management between pharmacies and primary care providers using real-world data exchange between providers and experimental bundled payment. This was a pragmatic, quasi-experimental controlled trial. We collected patient-level data from primary care prescription claims and Electronic Medical Record databases, a pharmacy claims database, and patient telephone surveys at several time points. The primary outcomes were changes in blood pressure and total cholesterol. We used matched controls with difference-in-differences estimators in a Generalized Linear Model (GLM) and controlled interrupted time series (CITS). We collected additional data for economic and qualitative studies. A total of 6 Primary Care Units, 20 pharmacies, and 203 patients entered the study. We were not able to observe significant differences in the effect of intervention vs. control. We experienced challenges that required creative strategies. This real-world trial was not able to show effectiveness, likely due to limitations in the primary care technology which affected the sample size. It offers, however, valuable lessons on methods, strategies, and data sources, paving the way for more real-world effectiveness trials to advance value-based healthcare.