With the Affordable Care Act revolutionizing the US health care system, the importance of collecting clinical, demographic, operational, and utilization data has exponentially increased for community health centers (CHC). Data collection of gender and gender identity presents a unique set of challenges for medical settings. One central challenge is the conflict between, on one hand, the need to know and use patients' preferred names, gender identities, and pronouns to establish trust and safety and, on the other hand, institutional requirements to know and use patients' legal names and gender markers with insurance companies and pharmacies. This essay examines how a community-based LGBTQ community health center, Lyon-Martin Health Services, collects and reports data about gender identity and how this process has changed over time. Lyon-Martin strongly supports the use of the two-step gender data collection method, which allows clinicians to have necessary information related to patients' anatomy-based health care while simultaneously honoring and respecting patients' gender identity and preferred pronouns. Collecting precise information about patient sex and gender is vital to providing not only respectful care but also medically appropriate care. The ability to quantify and justify the services provided by CHCs is a key part of keeping clinics open and thriving, from securing grant support to implementing internal quality improvement efforts to provide the best care for trans* patients. The shift toward electronic medical records and electronic practice management systems is also highlighted, including billing and clinical practice challenges due to narrowed gender options written into practice-management and billing software.