The adaptive potential of plastic phenotypes relies on combined developmental responses. Here, we investigated how manipulation of developmental conditions related to foraging mode in Megaleporinus macrocephalus fish induces plastic responses at different levels: 1) functional modularity of skull bones, 2) biomechanical properties of the chondrocranium using Finite Element Models, 3) bmp4 expression levels, used as a proxy for molecular pathways involved in bone responses to mechanical load. We identified new modules in the experimental groups, suggesting increased integration in head bone elements associated with the development of subterminal and upturned mouths, which are major features of Megaleporinus plastic morphotypes released in the lab. Plastic responses in head shape involved differences in the magnitude of mechanical stress, which seem restricted to certain chondrocranium regions. Three bones represent a ‘mechanical unit’ related to changes in mouth position induced by foraging mode, suggesting that functional modularity might be enhanced by specific regions responding to load. Differences in bmp4 expression levels between plastic morphotypes indicate associations between molecular signaling pathways and biomechanical responses to load. Our results offer a multilevel perspective of epigenetic factors involved in plastic responses, expanding our knowledge about mechanisms of developmental plasticity that originate novel complex phenotypes.