Although the knowledge of the skeletal morphology of bees has progressed enormously, a corresponding advance has not happened for the muscular system. Most of the knowledge about bee musculature was generated over 50 years ago, well before the digital revolution for anatomical imaging, including the application of microcomputed tomography. This technique, in particular, has made it possible to dissect small insects digitally, document anatomy efficiently and in detail, and visualize these data three dimensionally. In this study, we document the skeletomuscular system of a cuckoo bee, Thyreus albomaculatus and, with that, we provide a 3D atlas of bee skeletomuscular anatomy. The results obtained for Thyreus are compared with representatives of two other bee families (Andrenidae and Halictidae), to evaluate the generality of our morphological conclusions. Besides documenting 199 specific muscles in terms of origin, insertion, and structure, we update the interpretation of complex homologies in the maxillolabial complex of bee mouthparts. We also clarify the complicated 3D structure of the cephalic endoskeleton, identifying the tentorial, hypostomal, and postgenal structures and their connecting regions. We describe the anatomy of the medial elevator muscles of the head, precisely identifying their origins and insertions as well as their homologs in other groups of Hymenoptera. We reject the hypothesis that the synapomorphic propodeal triangle of Apoidea is homologous with the metapostnotum, and instead recognize that this is a modification of the third phragma. We recognize two previously undocumented metasomal muscle groups in bees, clarifying the serial skeletomusculature of the metasoma and revealing shortcomings of Snodgrass' “internal–external” terminological system for the abdomen. Finally, we elucidate the muscular structure of the sting apparatus, resolving previously unclear interpretations. The work conducted herein not only provides new insights into bee morphology but also represents a source for future phenomic research on Hymenoptera.