Muscle loading is known to influence skeletal morphology. Therefore, modification of the biomechanical environment is expected to cause coordinated morphological changes to the bony and cartilaginous tissues. Understanding how this musculoskeletal coordination contributes to morphological variation has relevance to health sciences, developmental biology, and evolutionary biology. To investigate how muscle loading influences skeletal morphology, we replicate a classic in ovo embryology experiment in the domestic chick (Gallus gallus domesticus) while harnessing modern methodologies that allow us to quantify skeletal anatomy more precisely and in situ. We induced rigid muscle paralysis in developing chicks mid‐incubation, then compared the morphology of the cranium and mandible between immobilized and untreated embryos using microcomputed tomography and landmark‐based geometric morphometric methods. Like earlier studies, we found predictable differences in the size and shape of the cranium and mandible in paralyzed chicks. These differences were concentrated in areas known to experience high strains during feeding, including the jaw joint and jaw muscle attachment sites. These results highlight specific areas of the skull that appear to be mechanosensitive and suggest muscles that could produce the biomechanical stimuli necessary for normal hatchling morphology. Interestingly, these same areas correspond to areas that show the greatest disparity and fastest evolutionary rates across the avian diversity, which suggests that the musculoskeletal integration observed during development extends to macroevolutionary scales. Thus, selection and evolutionary changes to muscle physiology and architecture could generate large and predictable changes to skull morphology. Building upon previous work, the adoption of modern imaging and morphometric techniques allows richer characterization of musculoskeletal integration that empowers researchers to understand how tissue‐to‐tissue interactions contribute to overall phenotypic variation.