Rapeseed press-cake (RPC) is a byproduct of rapeseed oil production, rich in proteins and fiber. The aim of this study was to investigate the impact of cold pressed RPC, RPC fiber isolate and RPC alkaline extract on the formation of acrylamide and 5-hydroxymethylfufural (HMF) in cookies. Both compounds were influenced by the ingredients: the addition of RPC led to a significant dose-dependent increase of HMF in the cookies and to an increase of acrylamide up to 66.9%. On the contrary, acrylamide concentration was reduced down to 39.6% in presence of the alkaline extract and down to 4.4% in the presence of the fiber extract. The Michael addition of free amino acids to acrylamide was further investigated by high-resolution mass spectrometry (HRMS) revealing that cysteine was the preferred nucleophile for acrylamide elimination.