ObjectivesHealth systems must rapidly move knowledge into practice to address disparities impacting sexual and gender minority (SGM) patients. This qualitative study explores barriers and facilitators that arose during an initiative to improve care for SGM patients in federally qualified health centres (FQHCs) from the perspectives of FQHC staff.DesignCross-sectional qualitative content analysis, using a general inductive approach, of secondary data from transcripts of intervention events offered to FQHC staff and semistructured interviews with staff and FQHC leadership during the intervention.Setting10 FQHCs from nine states in the USA.ParticipantsFQHC quality improvement (QI) and clinical care staff, and leaders at each FQHC.InterventionsThe transforming care for lesbian, gay, bisexual and transgender people QI initiative combined two evidence-based programmes, Learning Collaborative (LC) and Project Extension for Community Healthcare Outcomes (ECHO), to assist primary care health centres in developing capacity to identify SGM patients, monitor their health and care, and improve disparities.Primary and secondary outcome measuresThe primary outcome was identification of barriers and facilitators to implementing initiatives to improve care for SGM patients. The secondary outcome was clarification of how intervention participants used Project ECHO sessions versus LC meetings to obtain information that influenced implementation of the initiative at their FQHC.ResultsBarriers and facilitators mapped to two major themes: ‘Clinical’ (patients’ health, wellness, and available treatment) and Health Systems and Institutional Culture (FQHC operations, and customs and social institutions within the FQHCs and in the external environment). Common ‘Clinical’ inquiries were for assistance with behavioural health, pre-exposure prophylaxis and transgender hormone therapy. Prevalent facilitators included workflow change and staff training, while adapting electronic health records for data collection, decision support and data extraction was the most prevalent barrier.ConclusionsProject ECHO and LC provided complimentary forums to explore clinical and operational changes needed to improve care for SGM at FQHCs.