Anthraquinone residues in tea have been linked to atmospheric deposition. However, anthraquinones can also be biosynthesized in plants. In this work, we report on a sample-driven and GC-MS/MS-based analytical strategy to differentiate between endogenous and exogenous anthraquinones in dried walnut (Juglans regia) leaves. Anthraquinone and seven of its derivatives were quantified in 9 dried and 128 fresh samples of leaves from walnut and other deciduous trees from three different countries and nine sampling sites. The drying of walnut leaves in a hot-air electric oven eliminated 80% of anthraquinone concentration. Among the fresh walnut leaf samples, 94% exceeded the 0.01 mg/kg maximum residue limit of anthraquinone, with values up to 0.3 mg/kg. Most derivatives were also present above 0.01 mg/kg. However, in the leaves from other deciduous trees, the compounds were much lower than 0.01 mg/kg. We conclude that the low anthraquinone base levels in most samples may result from atmospheric pollution, whereas the higher anthraquinone residues in walnut leaves likely have an endogenous origin.