The objective of this study was to identify potentially remaining CeD-active peptides in the hydrolyzed and fermented food products BME, barley malt vinegar (BMV), and soy sauce with high resolution untargeted nanoLC-MS/MS method. Secondly, we aimed to quantitate the absolute concentrations of selected CeD-active peptides in the samples by targeted nanoLC-MS/MS with SIDA. The knowledge of the remaining concentrations of CeD-active peptides in fermented and hydrolyzed products enables a more reliable scientific basis for risk assessment of such food products.