2-tert-butyl-1,4-benzoquinone (TBBQ), a degradation product of lipid antioxidant Tert-Butylhydroquinone (TBHQ), is a new hazardous compound in foods. This study investigated whether co-ingestion of dietary protein and TBBQ can alleviate the toxicity of TBBQ. The results indicated that soy protein isolate, whey protein isolate, and rice protein significantly reduced the residual amount of TBBQ during simulated gastrointestinal digestion. This result was attributed to the excellent elimination capacity of the released amino acids for TBBQ through formation of adducts. Among 20 amino acids, histidine, lysine, glycine, and cysteine showed better elimination capacity for TBBQ; they can eliminate 92.1%, 89.4%, 86.1%, and almost 100%, respectively, in 5 min at pH 8.0. Further study indicated that amino acids with lower ionization constant exhibited greater TBBQ elimination capacity. In addition, incubation of the cells with 50 μM TBBQ for 12 h decreased the cell viability to 28.95 ± 3.25%; while amino acids intervention was involved in the alleviation of TBBQ cytotoxicity via decreasing ROS. Particularly, cysteine showed 100 times more TBBQ detoxifying capacity than other amino acids. This work could provide a theoretical basis for the potential application of amino acids for detoxifying TBBQ in the food industry.