Despite growing interest in ancient wheat varieties, the functional and nutritional properties of einkorn (Triticum monococcum) in cereal-based foods remain not fully elucidated. This study examined the chemical composition and functional properties of wholegrain einkorn pasta through cooking and simulated gastrointestinal digestion, comparing it with conventional Triticum durum wheat pasta. While sharing similar macronutrient profiles, einkorn pasta demonstrated higher retention of key compounds including phenolics, tocopherols, and phytosterols throughout cooking and in vitro digestion. Notable findings include enhanced prebiotic activity specifically targeting bifidobacteria populations and preserved antioxidant capacity despite thermal processing. These results demonstrated einkorn’s potential as a functional food ingredient, suggesting its capacity to deliver enhanced nutritional benefits through its unique matrix properties. Our findings provide mechanistic insights into ancient grain functionality in modern food applications, with implications for developing nutritionally enhanced pasta products.