Altered gravity conditions, such as experienced by organisms during spaceflight, are known to cause transcriptomic and proteomic changes. We describe the proteomic changes in whole adult Drosophila melanogaster (fruit fly) but focus specifically on the localized changes in the adult head in response to chronic hypergravity (3 g) treatment. Canton S adult female flies (2 to 3 days old) were exposed to chronic hypergravity for 9 days and compared with 1 g controls. After hypergravity treatment, either whole flies (body + head) or fly-head-only samples were isolated and evaluated for quantitative comparison of the two gravity conditions using an isobaric tagging liquid chromatography-tandem mass spectrometry approach. A total of 1948 proteins from whole flies and 1480 proteins from fly heads were differentially present in hypergravity-treated flies. Gene Ontology analysis of head-specific proteomics revealed host immune response, and humoral stress proteins were significantly upregulated. Proteins related to calcium regulation, ion transport, and ATPase were decreased. Increased expression of cuticular proteins may suggest an alteration in chitin metabolism and in chitin-based cuticle development. We therefore present a comprehensive quantitative survey of proteomic changes in response to chronic hypergravity in Drosophila, which will help elucidate the underlying molecular mechanism(s) associated with altered gravity environments.