Since March 2019, a non-communicable diseases program has been established at hospital level, with enrollment and clinical reassessment every 6 months. Since July 2023, monthly enrollment and visits have also been conducted at health center level. This study aimed at assessing the adherence to scheduled follow-up visits following the decentralization of the integrated NCDs program from Hospital to Health Center level and investigate factors influencing follow-up adherence. The study was performed in a rural district in Iringa Region, Tanzania. Adherence was measured at both levels. Multivariate regression analysis was conducted to describe socio-demographic and clinical factors influencing attendance at the 6-month hospital-level visit. Among 2198 patients enrolled at the hospital level, weighted adherence over 42 months was 40.8% (95% CI 39.0–42.6%) at the 6-month visit. Multivariate analysis revealed that as the distance from the hospital increased, the probability of attendance decreased (OR 0.17; 95% CI: 0.08–0.39). Among 571 patients enrolled at the residence level, adherence over the first 10 months of program implementation was 91.6% (90.4–92.8%). The findings showed that distance was by far the most important barrier to follow-up adherence and suggested that decentralizing the program from the hospital to peripheral health centers may ensure high follow-up rates.