BACKGROUND: Secure messaging (SM) between patients and primary care teams has expanded care access but may impact other clinical encounters. OBJECTIVE: To study associations between SM use and primary care in-person and telephone visits in the Veterans Health Administration (VHA). DESIGN: The SM feature of VHA's patient portal, MyHealtheVet, supports asynchronous communication between patients and primary care teams. To study the impact of SM on in-person and telephone visits, two analyses were performed: (1) a retrospective pre-/post-analysis comparing changes after initiating SM use and (2) a difference-in-difference comparison among SM users and non-users 1 year before and after index SM use. Matching to non-users was by primary care team, demographics, and predicted propensity of SM use by Nosos comorbidity score and drive time to clinic. PATIENTS: In 2016, 154,053 Veterans initiated SM from all primary care patients (N = 5,891,893); 25,683 were propensity-matched to controls (N = 49,266) from the same primary care team not using SM. MAIN MEASURES: Primary care provider in-person visits and telephone contacts between patients and their primary care team were assessed 1 year prior and post index SM. KEY RESULTS: Overall, primary care in-person visits decreased 13.3% (p < 0.0001); telephone visits increased 13.5% (p < 0.0001). In the matched analysis, in-person primary care visits decreased by 16.0% (p < 0.0001) by SM users and 9.9% (p < 0.0001) among controls, resulting in a across-group decrease of 6.1% in-person visits after SM initiation. Telephone visits increased by 11.0% (p < 0.0001) for SM users and 4.5% for controls (p < 0.0001) resulting in an across-group increase of 6.5% telephone visits after SM initiation. CONCLUSIONS: Use of SM was associated with decreased in-person visits and increased telephone visits. This may improve clinic appointment availability, while increasing time commitments for providers for nontraditional forms of access.