The whole meal flour of wheat is rich in phenolic acids, which provide a relevant antioxidant activity to food products. Aim of this research was to assess the influence of processing on phenolic acid content and antioxidant activity of whole meal flour water biscuits and puffed kernels of einkorn and bread wheat. To this end, the evolution of syringaldehyde, ferulic, vanillic, syringic, p-coumaric, phydroxybenzoic, and caffeic acids was studied during manufacturing. Overall, from flour to water biscuit, the total soluble conjugated phenolic acids increased slightly in einkorn, while the insoluble bound phenolic acids decreased in all the accessions as a consequence of losses during the mixing step. In the puffed kernels, instead, the total soluble conjugated phenolic acids increased markedly, while the bound phenolics did not show any clear change, evidencing their high thermal stability. The antioxidant activity, measured by FRAP and ABTS, increased during processing and was highest under the most drastic puffing conditions.