BACKGROUND: Over the past decade, the prevalence of stunting has been close to 37% in children aged <5 years in Indonesia. The Baduta program, a multicomponent package of interventions developed by the Global Alliance for Improved Nutrition, aims to improve maternal and infant nutrition in Indonesia. OBJECTIVE: This study aims to assess the impact of the Baduta program, a package of health system strengthening and behavior change interventions, compared with the standard village health services on maternal and child nutrition. METHODS: The impact evaluation uses a cluster randomized controlled trial design with 2 outcome assessments. The first uses cross-sectional surveys of mothers of children aged 0-23 months and pregnant women before and after the interventions. The second is a cohort study of pregnant women followed until their child is 18 months from a subset of clusters. We will also conduct a process evaluation guided by the program impact pathway to assess coverage, fidelity, and acceptance. The study will be conducted in the Malang and Sidoarjo districts of East Java, Indonesia. The unit of randomization is the subdistricts. As random allocation of interventions to only 6 subdistricts is feasible, we will use constrained randomization to ensure balance of baseline covariates. The first intervention will be health system strengthening, including the Baby-Friendly Hospital Initiative, and training on counseling for appropriate infant and young child feeding (IYCF). The second intervention will be nutrition behavior change that includes Emo-Demos; a national television (TV) advertising campaign; local screening TV spots; a free, text message service; and promotion of low-cost water filters and hygiene practices. The primary study outcome is child stunting (low length-for-age), and secondary outcomes include length-for-age Z scores, wasting (low weight-for-length), anemia, child morbidity, IYCF indicators, and maternal and child nutrient intakes. The sample size for each cross-sectional survey is 1400 mothers and their children aged <2 years and 200 pregnant women in each treatment group. The cohort evaluation requires a sample size of 340 mother-infant pairs in each treatment group. We will seek Gatekeeper consent and written informed consent from the participants. The intention-to-treat principle will guide our data analysis, and we will apply Consolidated Standards of Reporting Trials guidelines for clustered randomized trials in the analysis. RESULTS: In February 2015, we conducted a baseline cross-sectional survey on 2435 women with children aged <2 years and 409 pregnant women. In February 2017, we conducted an end-line survey on 2740 mothers with children aged <2 years and 642 pregnant women. The cohort evaluation began in February 2015, with 729 pregnant women, and was completed in December 2016. CONCLUSIONS: The results of the program evaluation will help guide policies to support effective packages of behavior change interventions to prevent child stunting in Indonesia. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR1-10.2196/18521.