Seafood is traded globally and is increasingly vulnerable to mislabeling and illegal, unregulated, and unreported (IUU) harvesting. These illicit activities prevail within the Manila clams (Ruditapes philippinarum) industry in the Tagus estuary (TE) in Portugal. This scenario prompted the use of elemental fingerprints (EF) of bivalve shells to confirm (or refute) claims on the geographic origin of this pricey seafood. To expose fraudulent practices, we mimicked real case scenarios and assessed the EF of R. philippinarum shells from three Portuguese estuaries: Ria de Aveiro (RAv), TE, and the Sado estuary (SE), as well as from two blind samples (B1 and B2) suspected of having been illegally harvested from TE, but mislabeled as originating from SE. Two reference models were developed using the EF of specimens from RAv, TE, and SE using CAP and Random Forests (RF). Both models confirmed the geographic origin of these clams (100% accuracy for CAP and 97.8% for RF). The same models predominantly allocated specimens from B1 and B2 to TE (93.3% and 100% for CAP; 100% and 93.3% for RF, respectively). Manganese and Phosphorus contributed to the classification of reference models, being present in high levels in the shells of clams from TE, B1 and B2, thereby being key for the allocation of blind samples to TE. This study confirms the potential of using EF of bivalve shells to trace the geographic origin of Manila clams under real-case scenarios, making it possible to strengthen the fighting against the mislabeling of seafood and IUU fishing.