Nanosized materials may produce adverse physiological effects or potential health risks due to their unique physical and chemical properties. Herein, the universal presence of fluorescent carbon dots (CDs) in commercial beers was confirmed through a systematic survey. The beer CDs were roughly spherically shaped in appearance and emitted bright blue fluorescence under ultraviolet light with quantum yields (QYs) ranging from 1.42% to 3.92%. Furthermore, digestion, biodistribution, and cytotoxicity assessments of CDs from Snow beer were conducted as an example. The CDs were significantly quenched during in vitro digestion. The dynamic distribution of CDs in mice showed that they easily accumulated in the intestine and liver, and more importantly, the beer CDs were found in the brain, which indicated that they were able to cross the blood–brain barrier. Acute toxicity of the beer CDs was evaluated using BALB/c mice, and the results revealed that the biochemical parameters of mice after administration of a single dose of 2 g kg−1 body weight were almost same as those of the control groups. Histological analysis showed no obvious organ damage in the tested mice. The in vitro results indicated that CDs dispersed onto both the cell membrane and the cytoplasm of MC3T3-E1 cells, alter the cell cycle progression, and caused cell apoptosis at high doses. This work reports the potential risk of CDs in beer and provides valuable information regarding CDs in food.