Aim of this research was to study the evolution of heat damage, phenolic acid content and in vitro antioxidant capacity of whole meal einkorn water biscuits baked at 205 °C for increasing times (10 min steps) from 25 to 75 min. The heat damage was gauged by determining furosine, hydroxymethylfurfural (HMF), furfural and glucosylisomaltol (GLI) contents. Furosine increased up to 50 min baking, when HMF started to form; furfural augmented only after 65 min treatment, whereas GLI did not change. An unknown compound, apparently related to the severity of the heat load, aroses through the aldolic condensation of HMF with the acetone used for the extraction of phenolic acids; hence the use of acetone-based solvents in thermally processed cereal products should be avoided. The conjugated phenolic acids ferulic, vanillic, syringic, p-coumaric, p-hydroxybenzoic and syringaldehyde and the bound phenolic acids ferulic, p-coumaric, syringic, and p-hydroxybenzoic were identified in water biscuits. The stronger heating treatments led to an increase of the soluble conjugated compounds, but did not influence the bound fraction. The in vitro antioxidant capacity of water biscuits augmented significantly as baking time increased, likely for the formation of antioxidant compounds as a consequence of heat damage.