Suboptimal infant young child feeding practices are frequently reported globally, including in Indonesia. This analysis examined the impact of a package of behaviour change interventions on breastfeeding practices in Malang and Sidoarjo Districts, East Java Province, Indonesia. The BADUTA study (which in the Indonesian Language is an acronym for BAwah DUa TAhun, or children aged less than 2 years) was an impact evaluation using a cluster-randomized controlled trial with two parallel treatment arms. We conducted household surveys in 12 subdistricts from Malang and Sidoarjo. We collected information from 5175 mothers of children aged 0-23 months: 2435 mothers at baseline (February 2015) and 2740 mothers at endline (January to February 2017). This analysis used two indicators for fever and diarrhoea and seven breastfeeding indicators (early initiation of breastfeeding, prelacteal feeding, exclusive breastfeeding under 6 months, predominant breastfeeding, continued breastfeeding, age-appropriate breastfeeding and bottle-feeding). We used multilevel logistic regression analysis to assess the effect of the intervention. After 2 years of implementation of interventions, we observed an increased odds of exclusive breastfeeding under 6 months (adjusted odds ratio [aOR] = 1.85; 95% confidence interval [CI]: 1.35-2.53) and age-appropriate breastfeeding (aOR = 1.39; 95% CI: 1.07-1.79) in the intervention group than in the comparison group, at the endline survey. We found significantly lower odds for prelacteal feeding (aOR = 0.52; 95% CI: 0.41-0.65) in the intervention than in the comparison group. Our findings confirmed the benefits of integrated, multilayer behaviour change interventions to promote breastfeeding practices. Further research is required to develop effective interventions to reduce bottle use and improve other breastfeeding indicators that did not change with the BADUTA intervention.