BackgroundMinority social status determined by religion, caste and tribal group affiliations, are usually treated as independent dimensions of inequities in India. This masks relative privileges and disadvantages at the intersections of religion-caste and religion-tribal group affiliations, and their associations with population health disparities.MethodsOur analysis was motivated by applications of the intersectionality framework in public health, which underlines how different systems of social stratification mutually inform relative access to material resources and social privilege, that are associated with distributions of population health. Based on this framework and using nationally representative National Family Health Surveys of 1992–93, 1998–99, 2005–06, 2015–16 and 2019–21, we estimated joint disparities by religion-caste and religion-tribe, for prevalence of stunting, underweight and wasting in children between 0–5 years of age. As indicators of long- and short-term growth interruptions, these are key population health indicators capturing developmental potential of children. Our sample included Hindu and Muslim children of <  = 5 years, who belonged to Other (forward) castes (the most privileged social group), Other Backward Classes (OBCs), Schedule Castes (SCs) and Schedule Tribe (STs). Hindu-Other (forward) caste, as the strata with the dual advantages of religion and social group was specified as the reference category. We specified Log Poisson models to estimate multiplicative interactions of religion- caste and religion-tribe identities on risk ratio scales. We specified variables that may be associated with caste, tribe, or religion, as dimensions of social hierarchy, and/or with child growth as covariates, including fixed effects for states, survey years, child’s age, sex, household urbanicity, wealth, maternal education, mother’s height, and weight. We assessed patterns in growth outcomes by intersectional religion-caste and religion-tribe subgroups nationally, assessed their trends over the last 30 years, and across states.FindingsThe sample comprised 6,594, 4,824, 8,595, 40,950 and 3,352 Muslim children, and 37,231, 24,551, 35,499, 1,87,573 and 171,055 Hindu children over NFHS 1, 2, 3, 4, and 5, respectively. As one example anthropometric outcome, predicted prevalence of stunting among different subgroups were as follows- Hindu Other: 34.7% (95%CI: 33.8, 35.7), Muslim Other: 39.2% (95% CI: 38, 40.5), Hindu OBC: 38.2 (95%CI: 37.1, 39.3), Muslim OBC: 39.6% (95%CI: 38.3, 41), Hindu SCs: 39.5% (95%CI: 38.2, 40.8), Muslims identifying as SCs: 38.5% (95%CI: 35.1, 42.3), Hindu STs: 40.6% (95% CI: 39.4, 41.9), Muslim STs: 39.7% (95%CI: 37.2, 42.4). Over the last three decades, Muslims always had higher prevalence of stunting than Hindus across caste groups. But this difference doubled for the most advantaged castes (Others) and reduced for OBCs (less privileged caste group). For SCs, who are the most disadvantaged caste group, the Muslim disadvantage reversed to an advantage. Among tribes (STs), Muslims always had an advantage, which reduced over time. Similar directions and effect sizes were estimated for prevalence of underweight. For prevalence of wasting, effect sizes were in the same range, but not statistically significant for two minority castes-OBCs and SCs.InterpretationHindu children had the highest advantages over Muslim children when they belonged to the most privileged castes. Muslim forward caste children were also disadvantaged compared to Hindu children from deprived castes (Hindu OBCs and Hindu SCs), in the case of stunting. Thus, disadvantages from a socially underprivileged religious identity, seemed to override relative social advantages of forward caste identity for Muslim children. Disadvantages born of caste identity seemed to take precedence over the social advantages of Hindu religious identity, for Hindu children of deprived castes and tribes. The doubly marginalized Muslim children from deprived castes were always behind their Hindu counter parts, although their differentials were less than that of Muslim-Hindu children of forward castes. For tribal children, Muslim identity seemed to play a protective role. Our findings indicate monitoring child development outcomes by subgroups capturing intersectional social experiences of relative privilege and access from intersecting religion and social group identities, could inform policies to target health disparities.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12939-023-01917-3.