ABSTRACT Background The COVID-19 pandemic prompted varied policy responses globally, with Latin America facing unique challenges. A detailed examination of these policies’ impacts on health systems is crucial, particularly in Bolivia, where information about policy implementation and outcomes is limited. Objective To describe the COVID-19 testing trends and evaluate the effects of quarantine measures on these trends in Cochabamba, Bolivia. Methods Utilizing COVID-19 testing data from the Cochabamba Department Health Service for the 2020–2022 period. Stratified testing rates in the health system sectors were first estimated followed by an interrupted time series analysis using a quasi-Poisson regression model for assessing the quarantine effects on the mitigation of cases during surge periods. Results The public sector reported the larger percentage of tests (65%), followed by the private sector (23%) with almost double as many tests as the public-social security sector (11%). In the time series analysis, a correlation between the implementation of quarantine policies and a decrease in the slope of positive rates of COVID-19 cases was observed compared to periods without or with reduced quarantine policies. Conclusion This research underscores the local health system disparities and the effectiveness of stringent quarantine measures in curbing COVID-19 transmission in the Cochabamba region. The findings stress the importance of the measures’ intensity and duration, providing valuable lessons for Bolivia and beyond. As the global community learns from the pandemic, these insights are critical for shaping resilient and effective health policy responses.