The need for a multisectoral approach to tackle stunting has gained attention in recent years. Baduta project aims to address undernutrition among children during their first 1000 days of life using integrated nutrition-specific and nutrition-sensitive interventions. We undertook this cohort study to evaluate the Baduta project’s effectiveness on growth among children under 2 years of age in two districts (Sidoarjo and Malang Districts) in East Java. Six subdistricts were randomly selected, in which three were from the intervention areas, and three were from the control areas. We recruited 340 pregnant women per treatment group during the third trimester of pregnancy and followed up until 18 months postpartum. The assessment of breastfeeding and complementary feeding practices used standard infant and young child feeding (IYCF) indicators in a tablet-based application. We measured weight and length at birth and every three-months after that. The enumerators met precision and accuracy criteria following an anthropometry standardization procedure. Among the breastfed children, the percentage of children who achieved the minimum dietary diversity score (DDS) and minimum acceptable diet (MAD) was higher for the intervention group than the comparison group across all age groups. The odd ratios were 3.49 (95% CI: 2.2–5.5) and 2.79 (95% CI: 1.7–4.4) for DDS and 3.49 (95% CI: 2.2–5.5) and 2.74 (95% CI: 1.8–5.2) for MAD in the 9–11 month and 16–18-month age groups, respectively. However, there was no significant improvement in growth or reduction in the prevalence of anemia. The intervention was effective in improving the feeding practices of children although it failed to show significant improvement in linear growth of children at 18 months of age.