Background: In August 2018 Lombok Island in Indonesia was hit by a 7 Richter scale earthquake. This study aimed to assess the effectiveness of comprehensive nutrition disaster rehabilitation, based on the holistic integrated early child development concept, on the growth and development of children under five. Methods: A community-based intervention was performed in the East Lombok district; four villages in two sub-districts were randomly allocated into intervention or control groups. Mothers of 6–49-month-old children in the intervention group (n = 240) attended parenting classes (twice weekly) and received shredded fish/liver/anchovy and optimized complementary feeding/food-based recommendations, developed using linear programming. Health staff from the public health center and teachers from early childhood education (ECE) centers delivered parenting sessions on health–nutrition and care–education. The control group (n = 240) received existing health services. Indicators measured at baseline and the end line point were weight, length/height, hemoglobin, feeding practices, psychosocial care (HOME) and maternal stress (SRQ). At the end line point, child development was assessed using BSID-III. Results: At the end line point, maternal stress and child morbidity (cough) were lower and dietary diversity (+1) in 6–23-month-old children, and weight-for-age Z-score (+0.26) and social emotional score (+10 points) in ≥24-month-old children were higher in the intervention group. Conclusions: The nutrition rehabilitation intervention delivered through ECE centers has a positive effect on the growth and development of children under five in post-disaster conditions.