In New York City, federally qualified health centers (FQHCs) are ideal partners for health departments because of their location in neighborhoods with high rates of HIV, hepatitis C virus (HCV) infection, and gonorrhea. Providers have experienced many barriers to following screening and treatment recommendations. In 2013, the New York City Department of Health and Mental Hygiene partnered with six FQHCs, representing 14 clinics, to make screening for HIV and HCV routine and increase adherence to gonorrhea treatment guidelines through education, electronic health record modification, and progress tracking. After one year, 12 of 14 clinics documented improvement in their HIV offer rate, and 11 clinics documented improvement in their HIV screening rate. Patients who were offered HIV screening increased from 26% at baseline to 56% at follow-up, and patients screened for HIV increased from 25% at baseline to 38% at follow-up. Most clinics improved their HIV screening rate, and progress suggests that local health departments can help FQHCs increase their HIV screening rates.