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Background Child undernutrition has remained a major public health problem. Preconception care is evident to improve pregnancy outcomes. However, the role of preconception care services in long-term child health outcomes is unknown.Objective To compare the nutritional status of preschool children born to women who received preconception care with children born to women who did not receive preconception care.Design This was an analytical cross-sectional study conducted 2 years after the end of the preconception care services provided.Settings Rural area in Nashik district, including two tribal and two non-tribal blocks. We conducted the study in collaboration with the government’s public health system.Participants All women desiring pregnancy were enrolled in July–August 2018 to receive preconception care. Women from two blocks received preconception care, while those from the other two blocks did not. Those women and their children were the participants.Primary and secondary outcomes for the present study Anthropometric nutritional assessment of the children and estimation of the Composite Index of Anthropometric Failure (CIAF). The association between risk factors and prevalence of CIAF was confirmed by multivariable modified Poisson regression models with robust variance.Results We contacted 4141 mother–offspring pairs. The proportion of the combination of stunting plus underweight was highest (35.18%), followed by triple failure (19.10%). Among the children born to mothers who received preconception care, 88.10% had some anthropometric failure, and among children born to mothers in the comparison group, 85.80% had some anthropometric failure (adjusted risk ratio (ARR) 0.99 (95% CI 0.97 to 1.02)). The incidence of some anthropometric failure among children of women residing in tribal areas was 94.38%, and among children of women residing in non-tribal areas, it was 82.54% (ARR 1.11 (95% CI 1.08 to 1.15)). Mothers of second or higher parity had a higher risk of having a child with some anthropometric failure (ARR 1.07 (95% CI 1.01 to 1.11)). Low birth weight babies had a higher risk (ARR 1.04 (95% CI 1.00 to 1.08)); boys had a higher risk (ARR 1.04 (95% CI 1.01 to 1.07)) and risk increased with age.Conclusions Numerous factors, particularly residence in a tribal area, affect child nutritional status and mere preconception care for women may not prevent undernutrition among preschool children.