To manage the COVID‐19 pandemic, governments established certain stringency measures, such as lockdowns and traffic light systems. However, the response to the pandemic depended on the regions' preexisting capacities and underlying conditions. This study aims to determine the relationship between the COVID‐19 pandemic dynamics and the underlying regional healthcare system's structure in Ecuador, using three dependent variables—the number of COVID‐19 cases, the COVID‐19 prevalence rate at the cantonal level, and the daily deaths resulting from COVID‐19 at the provincial level—for three phases: isolation, social distancing, and contingency. Using daily COVID‐19 data and cantonal (provincial) level variables, a negative binomial model and a tobit model were estimated to analyze the determinants of the number of COVID‐19 cases and the prevalence rate, respectively. The results show a positive relationship between primary and secondary health centers and the number of infected people, implying that it is possible to make more diagnoses when the health infrastructure is more developed. As for COVID‐19 deaths, primary health centers are associated with a low number of daily deaths whereas secondary health centers are associated with a higher number of daily deaths, implying the transfer of severe COVID‐19 cases to cantons with secondary health centers. More affluent cantons had more COVID‐19 cases and deaths. Stringency measures, such as the traffic light system, were effective in managing the pandemic. The geographical proximity between cantons and the nature of economic activities (essential versus non‐essential) also impacted the spread of the virus.