Non-communicable diseases like hypertension cause substantial morbidity and mortality in low- and middle-income countries, where limited access to high-quality care contributes to millions of preventable deaths annually. Traditional assessments of health system performance often rely on structural indicators and cross-sectional, overlooking patient experiences and care processes. In Latin America, amid rising cardiovascular disease, longitudinal tools are needed to guide improvements in healthcare delivery models, particularly for chronic diseases such as hypertension. The NCD e-Cohort is a prospective, longitudinal, mixed-mode (in-person and phone) survey designed to assess health system quality in Latin America. Developed by the QuEST Network, it integrates validated and locally tailored items aligned with the Lancet Global Health Commission's framework. Key domains include competent care, user experience, health outcomes, confidence in the health, economic impacts, and care pathways. About 600 hypertensive patients aged 35+ will be recruited from sentinel sites in Uruguay (CESCAS) and Peru (CRONICAS), with 300 participants per site. Data will be collected for one year, capturing real-time information on patient journeys and health system performance. This study advances hypertension care assessment by embracing the care-cascade approach and capturing dynamic patient-provider interactions, continuity, and treatment evolution. Although participant attrition may pose challenges, the frequent data collection minimises recall bias. The NCD e-Cohort will generate timely, actionable evidence to inform patient-centred policies and strengthen health systems in the region. Leveraging mobile technology enhances feasibility, scalability, and adaptability, potentially extending this approach to other chronic conditions.