Understanding and acceptance of evolution are often assumed to be associated; however, empirical evidence from students attending Islamic boarding schools (pesantren) in Indonesia remains limited and rarely accounts for differences in school contexts. This study aimed to describe students' understanding and acceptance of evolutionary concepts, examine the relationship between these two variables within each school, and determine whether this relationship differed across schools. A cross-sectional correlational design was employed, involving 127 students from three Islamic boarding schools (School A, n = 50; School B, n = 34; and School C, n = 43). Evolution acceptance was measured using the Measure of Acceptance of the Theory of Evolution (MATE) 2.0, while understanding was assessed using the multiple-choice test developed by Rutledge and Warden. Data were analyzed using Pearson's and Spearman's correlation coefficients, followed by school-specific regression analyses. Subsequently, multiple regression analysis was conducted with understanding, school, and the Understanding × School interaction as predictors, using robust standard errors. A significant positive association between understanding and acceptance was found only in School B (r = .81, p < .001), whereas no association was detected in School A (r = .03) or School C (r = .06). The regression model incorporating the Understanding × School interaction was statistically significant, F(2, 121) = 19.96, p < .001. These findings indicate that the relationship between understanding and acceptance of evolution is contingent on school context, suggesting that an overall pooled correlation coefficient may not adequately represent the patterns observed across individual schools.