Severe weather events exacerbate existing health disparities due to poorly managed non-communicable diseases (NCDs). Our objective is to understand the experiences of staff, providers, and administrators (employees) of Federally Qualified Health Centers (FQHCs) in Puerto Rico and the US Virgin Islands (USVI) in providing care to patients living with NCDs in the setting of recent climate-related extreme events. We used a convergent mixed-methods study design. A quantitative survey was distributed to employees at 2 FQHCs in Puerto Rico and the USVI, assessing experience with disasters, knowledge of disaster preparedness, the relevance of NCDs, and perceived gaps. Qualitative in-depth interviews explored their experience providing care for NCDs during recent disasters. Quantitative and qualitative data were merged using a narrative approach. Through the integration of quantitative and qualitative data, we recognize: (1) significant gaps in confidence and preparedness of employees with a need for more training; (2) challenges faced by persons with multiple NCDs, especially cardiovascular and mental health disorders; and (3) most clinicians do not discuss disaster preparedness with patients but recognize their important role in community resilience. With these results, we recommend strengthening the capacity of FQHCs to address the needs of their patients with NCDs in disasters.