Adolescence is a nutritionally vulnerable and critical life stage. However, few programs and policies focus on improving adolescent nutrition in Indonesia. To address this gap, we implemented a gender-responsive package of interventions: (1) breakfast and weekly iron-folic acid supplementation (WIFS), (2) a school-based nutrition education program, and (3) a social behavior change communication strategy. We surveyed 514 adolescents at baseline (2019) and endline (2020) in Klaten and Lombok Barat districts in Indonesia. The survey included a knowledge assessment on nutrition, as well as indicators of attitudes and behaviors on diet, physical activity, and WIFS. We employed multivariable linear and logistic regression to test for pre–post intervention differences. Overall knowledge was significantly higher post-intervention (β: 3.3; 95% confidence interval [CI]: 2.6, 3.9). Diet diversity was high at both timepoints, however, at post-intervention there was significantly higher odds of consuming vitamin A-rich fruits and vegetables (Odds Ratio [OR]: 1.5; 95% CI: 1.1, 2.0) and lower odds of consuming sugar-sweetened beverages (OR: 0.4; 95% CI: 0.3, 0.5). Post-intervention, there was higher odds of reporting 60 min of daily physical activity (OR: 2.3; 95% CI: 1.7, 3.2) and WIFS among girls (OR: 6.7; 95% CI: 1.5, 30.9). The package of interventions may be a promising first step to improving adolescent nutrition in Indonesia.