Introduction: Puerto Ricos network of Federally Qualified Health Centers (FQHCs), which consists of 22 centers with 86 satellite clinics, is the backbone of the island’s primary health care system. Therefore, it is extremely important to study the effect of the COVID-19 pandemic on the delivery of services and the adaptation strategies implemented to continue operations. The research Objectives were to identify, measure and describe the effect of the pandemic on the FQHCs’ continuity of operations, financial stability, and strategies implemented. Finally, we sought to develop recommendations to strengthen the FQHCs’ continuity of operations for future emergencies. Methods: A mixed research Methodology was utilized in which quantitative and qualitative approaches were combined. Of the 21 FQHCs that qualified for the study, 17, or 81.0%, provided the research team with data on service utilization, patients served, staff, operating costs, and revenue received from 2018 to 2020. Moreover, individual and group interviews were conducted with patients, members of the Board of Directors, community leaders, clinical staff, and senior management from a sample of seven FQHCs. We then triangulated the data and information collected from both components. Results: Puerto Rico’s FQHCs demonstrated great flexibility, adaptability, and innovative capacity during their response to the pandemic. The primary health care services provided played an important role in assisting, supporting, and mitigating the impact of COVID-19 on the health of thousands of vulnerable persons, families, and communities around the island. Conclusions: While there is clearly much work to be done to overcome this public health challenge, the current moment offers an opportunity for Puerto Rico’s local and state political leaders to use the creativity, innovations, and lessons learned from the FQHCs’ response to the COVID-19 pandemic to maintain and strengthen an equitable primary health care system that is resilient and accessible in the future.