Reducing multifactorial stunting is a priority for the 2025 WHO Global Nutrition Target. In the plant-based complementary diets of low-income countries, deficits in several growth-limiting micronutrients may contribute to stunting. Hence the intercorrelation between multiple micronutrients in terms of their intake and impact is important. Therefore, our aim was to develop a nutrient quality score using principal component analysis (PCA) in a sample of Indonesian infants at 6, 9 and 12 months of age and to evaluate the association of the scores with linear growth and stunting. At 6 months, 217 infants were recruited from Sumedang District, West Java, with 195 and 189 followed at 9 and 12 months of age, respectively. Complementary food intakes were assessed using 2-d weighed food records. Eight correlated nutrients (vitamin A, ascorbic acid, thiamine, riboflavin, niacin, Ca, Fe and Zn) were summarised using PCA into a single nutrient pattern that explained 56–65 % of the total variability. Nutrient quality scores were related to demographic, inflammation and complementary food indicator variables in hypothesised directions. While no significant relationships were apparent with linear growth, the odds of being stunted at ages 9 and 12 months was lower for infants with a higher nutrient quality score at 9 months (OR 0·75, 95 % CI 0·59, 0·95 and OR 0·69, 95 % CI 0·55, 0·88), respectively, for the fully adjusted models. A data-driven nutrient quality score is a valid tool to assess the influence of nutrient quality on stunting in at-risk infants.