Background: Diabetes mellitus (DM) and hypertension (HT) control under the Chronic Disease Management Program (Prolanis) is an important indicator of primary care performance in Indonesia. Objective: This study analyzed the level, trend, and between-facility disparity of the Controlled-Participant Ratio (RPPT) for DM and HT among registered Prolanis participants across 25 community health centers (Puskesmas) in Sleman Regency during 2024–2025. Methods: Using facility-level panel data (2024–2025), a binomial generalized linear mixed model (GLMM; random intercept for Puskesmas) with cluster-robust standard errors estimated the adjusted Controlled-Participant Ratio (RPPT) and between-year risk differences, with a paired Wilcoxon signed-rank test serving only as a robustness check. Results: The adjusted DM control proportion (7.6%) was higher than that of HT (3.5%) (p<0.001). Both conditions showed only slight between-year changes that were not statistically significant after accounting for facility clustering and overdispersion (DM +0.09 pp, p=0.83; HT +0.54 pp, p=0.053), and the disease×year interaction was not significant (p=0.18); a paired nonparametric robustness check indicated a consistent tendency toward HT improvement (p=0.028). Between-facility disparity was substantial, with a 23.1-fold gap for DM and a 10.0-fold gap for HT, with the lowest-performing facility differing by disease (Kalasan for DM and Cangkringan for HT). Conclusion: DM and HT control varied substantially across facilities. HT control remained below the national KBK performance target, whereas DM control met the target. The observed tendency toward HT improvement was not statistically robust, highlighting the need for targeted Prolanis strengthening and routine facility-level monitoring, particularly at persistently low-performing Puskesmas.