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Abstract The ontogeny of feeding is characterized by shifting functional demands concurrent with changes in craniofacial anatomy; relationships between these factors will look different in primates with disparate feeding behaviors during development. This study examines the ontogeny of skull morphology and jaw leverage in tufted (Sapajus) and untufted (Cebus) capuchin monkeys. UnlikeCebus,Sapajushave a mechanically challenging diet and behavioral observations of juvenileSapajussuggest these foods are exploited early in development. Landmarks were placed on three‐dimensional surface models of an ontogenetic series ofSapajusandCebusskulls (n = 53) and used to generate shape data and jaw‐leverage estimates across the tooth row for three jaw‐closing muscles (temporalis, masseter, medial pterygoid) as well as a weighted combined estimate. Using geometric morphometric methods, we found that skull shape diverges early and shape is significantly different betweenSapajusandCebusthroughout ontogeny. Additionally, jaw leverage varies with age and position on the tooth row and is greater inSapajuscompared toCebuswhen calculated at the permanent dentition. We used two‐block partial least squares analyses to identify covariance between skull shape and each of our jaw muscle leverage estimates.Sapajus, but notCebus, has significant covariance between all leverage estimates at the anterior dentition. Our findings show thatSapajusandCebusexhibit distinct craniofacial morphologies early in ontogeny and strong covariance between leverage estimates and craniofacial shape inSapajus. These results are consistent with prior behavioral and comparative work suggesting these differences are a function of selection for exploiting mechanically challenging foods inSapajus, and further emphasize that these differences appear quite early in ontogeny. This research builds on prior work that has highlighted the importance of understanding ontogeny for interpreting adult morphology.