Interest in ancient wheat species is growing because of their unique agronomic and nutritional qualities, and they could be potential sources of antioxidants. The aim of this research was to determine the total, bound, and free phenolic content (TP, FP, BP), the bound and free phenolic acid (BPA, FPA) content, and the phenolic acid (PA) composition of einkorn and emmer cultivars sourced from a two-year pesticide-free organic variety trial. TPs, FPs, and BPs were analyzed using spectrophotometry, and PAs were determined using HPLC/MS/MS. The results showed that highest mean TP, FP, and BP contents were found in an emmer cultivar, while generally, einkorn varieties had lower phytonutrient values than emmer and bread wheat control. Emmer had the highest TPA, FPA, and BPA contents, followed by control wheat and einkorn landraces. Our gap-filling research was the analysis of the individual PA values in all free and bound fractions. Ferulic acid was the predominant phenolic acid, followed by p-coumaric acid, syringic acid, sinapic acid, and p-hydroxybenzoic acid, whereas salicylic acid and caffeic acid had the lowest concentrations. In the future, we propose to continue this research to gain deeper insights into the changes in phytonutrient properties related to the growing conditions of these cultivars.