BACKGROUND: Rural patients with diabetes have difficulty accessing care and are at higher risk for poor diabetes management. Sustained use of patient portal features such as secure messaging (SM) can provide accessible support for diabetes self-management. OBJECTIVE: This study explored whether rural patients' self-management and glycemic control was associated with the use of SM. METHODS: This secondary, cross-sectional, mixed methods analysis of 448 veterans with diabetes used stratified random sampling to recruit a diverse sample from the United States (rural vs urban and good vs poor glycemic control). Administrative, clinical, survey, and interview data were used to determine patients' rurality, use of SM, diabetes self-management behaviors, and glycemic control. Moderated mediation analyses assessed these relationships. RESULTS: The sample was 51% (n=229) rural and 49% (n=219) urban. Mean participant age was 66.4 years (SD 7.7 years). More frequent SM use was associated with better diabetes self-management (P=.007), which was associated with better glycemic control (P<.001). Among rural patients, SM use was indirectly associated with better glycemic control through improved diabetes self-management (95% CI 0.004-0.927). These effects were not observed among urban veterans with diabetes (95% CI -1.039 to 0.056). Rural patients were significantly more likely than urban patients to have diabetes-related content in their secure messages (P=.01). CONCLUSIONS: More frequent SM use is associated with engaging in diabetes self-management, which, in turn, is associated with better diabetes control. Among rural patients with diabetes, SM use is indirectly associated with better diabetes control. Frequent patient-team communication through SM about diabetes-related content may help rural patients with diabetes self-management, resulting in better glycemic control.