This brief report describes the provision of early pregnancy loss (EPL) management in New York State Federally Qualified Health Centers (FQHCs) and barriers to providing this care. Office-based early pregnancy loss (EPL) care is safe and suitable to FQHCs, yet the prevalence of provision in FQHCs is unknown. We found that few New York FQHCs provided comprehensive EPL care. Supporting FQHCs to overcome barriers may expand access to EPL management in primary care and increase continuity and patient-centeredness.