Graviera Naxos, a renowned cheese with Protected Designation of Origin status, is crafted from a blend of cow, goat, and sheep milk. This study focused on assessing the Sr isotopic and multi-elemental composition of both the processed cheese and its ingredients, as well as the environmental context of Naxos Island, including samples of milk, water, soil, and feed. The objective was to delineate the geochemical signature of Graviera Naxos cheese and to explore the utility of Sr isotopes as indicators of geographic origin. The 87Sr/86Sr values for Graviera Naxos samples ranged from 0.70891 to 0.70952, indicating a relatively narrow range. However, the Sr isotopic signature of milk, heavily influenced by the feed, which originates from geologically distinct areas, does not always accurately reflect the local breeding environment. Multi-elemental analysis revealed variations in milk composition based on type and season; yet, no notable differences were found between raw and pasteurized milk. A mixing model evaluating the contributions of milk, sea salt, and rennet to the cheese’s Sr isotopic signature suggested a significant average contribution of 73.1% from sea salt. This study highlights the complexities of linking dairy products with their geographical origins and emphasizes the need for sophisticated geochemical authentication methods.