Purpose: Electronic medical records (EMRs) are central to Indonesia's digital health transformation, but adoption alone does not ensure that routinely collected data inform action. In Puskesmas, patient data should support continuity of care, service improvement, program management, and recognition of disease-risk patterns in communities. This study examined whether EMR implementation in Puskesmas in Jayapura City had progressed from electronic recording to organizational data use. Methods: We used an explanatory sequential mixed-methods design. A cross-sectional survey included 114 staff members from 14 Puskesmas in Jayapura City between May and July 2025. The survey measured reported EMR use, perceived ease of use, data security and quality, and the main implementation barrier. Semi-structured interviews with six management and frontline informants explored how staff used EMR data in routine work. Survey data were summarized using frequencies and percentages, and interview data were analyzed thematically to explain the quantitative patterns. Results: Most respondents reported using the EMR (93.9%), finding it easy to use (96.5%), having secure patient data (96.5%), and reporting good data quality (83.3%). The most frequently reported barriers were limited training (37.7%), system-integration difficulties (21.9%), and limited internet connectivity (20.2%). Interviews indicated that EMRs mainly supported registration, clinical recording, and patient flow; routine use of EMR data for program planning and management review remained limited. Training gaps, duplicate entry across non- interoperable systems, connectivity problems, and inadequate hardware kept staff focused on recording rather than analysis. Conclusion: Jayapura City's Puskesmas have established electronic recording, but not yet routine data-informed management. Puskesmas managers should institute regular data-review meetings, assign responsibility for interpreting indicators and following up decisions, and train staff beyond data entry. The City Health Office should support interoperability, infrastructure, and supervision of data use. Another agenda is to convert aggregated, privacy-protected patient information into locally relevant risk profiles that Puskesmas teams can discuss with village and kampung leaders, so clinical care is linked to community action that reduces recurring exposure and illness.