Medication therapy management (MTM) services, including targeted, pharmacist-delivered, tertiary prevention interventions, were provided to rural patients with chronic diseases via an academic-community partnership. The purpose of this investigation was to evaluate the overall program and pre/post patient outcomes from this four-year, multi-site collaboration. Five community health sites collaborated with a university-based MTM provider to deliver services in Arizona (2012–16). Eligible patients: were 18 or older (median 65 years); had a diagnosis of diabetes and/or hypertension; and resided in a rural community. Participants received an initial telephone consultation with the MTM pharmacist; follow-up consultations were conducted after 30 or 90 days for high- and low-risk patients, respectively. Community partner staff collected clinical data and addressed pharmacists’ recommendations. Descriptive analysis and bivariate analyses of pre- and post-intervention results were conducted. Most (n = 410, 70%) of the 577 participants receiving an initial and follow-up consultation with the MTM pharmacist had both diabetes and hypertension. These individuals showed statistically significant improvements in fasting blood glucose (p < 0.0001), hemoglobin A1C (p = 0.0082) and systolic blood pressure (p = 0.009) while those with only one condition did not demonstrate significant changes. While the pre/post changes in chronic disease control indicators were statistically significant, the clinical significance was low to moderate. Patients with both comorbid diabetes and hypertension experienced benefit from collaborative, targeted MTM pharmacist-delivered, tertiary prevention interventions in tandem with community-based pharmacy resources. This multi-site MTM program showed promise in increasing patients’ use of these services, yet effective strategies are needed to expand recruitment of eligible patients in the future.