Filtration methods for alcoholic fermented beverages often use filter aids such as diatomaceous earth (DE), which may contain elevated amounts of the heavy metals arsenic (As), lead (Pb), and cadmium (Cd). Here, we evaluated factors affecting transfer of these heavy metals from DE to beer and wine. A laboratory-scale filtration system was used to process unfiltered ale, lager, red wine, and white wine with three types of food-grade DE. Filtrate and DE were analyzed for heavy metals using ICP-MS, in addition to LC-ICP-MS for As-speciation analysis. Use of 2 g/L DE containing 5.4 mg/kg soluble inorganic As (iAs) for filtering beer and wine resulted in significant (p < 0.05) increases of 11.2–13.7 μg/L iAs in the filtered beverage. There was a significant (p < 0.05) effect from the DE quantity used in filtration on the transfer of iAs in all beverage types, whereas no alterations were observed for Pb and Cd levels. Methods to wash DE using water, citric acid, or EDTA all significantly (p < 0.05) reduced iAs concentrations, whereas only EDTA significantly reduced Pb levels. Cd concentrations were not affected by any wash method. These data indicate that specific steps can be taken to limit heavy-metal transfer from DE filter aids to beer and wine.