Rising demand for functional dairy products has stimulated interest in incorporating traditional fermented ingredients into modern food systems. This study investigated the use of traditional Greek trahanas as a functional ingredient in yogurt and evaluated its effects on physicochemical, microbiological, antioxidant-related, and sensory characteristics. Five formulations were produced: a control yogurt inoculated with a commercial yogurt starter culture, two starter-inoculated yogurts supplemented with 2% and 4% (w/w) trahanas, and two starter-free fermented dairy formulations supplemented with 2% and 4% (w/w) trahanas. All products were evaluated over 30 days of refrigerated storage (4 °C) in terms of pH evolution, lactose consumption, lactic acid production, protein content, total solids, syneresis, antioxidant activity, total phenolic content, microbial stability, and sensory properties. The trahanas-enriched yogurts inoculated with a starter culture exhibited enhanced acidification, higher protein and total solid contents, reduced syneresis, and increased antioxidant activity and phenolic content compared with the control and starter-free formulations. In particular, the 4% trahanas formulation inoculated with a commercial starter culture exhibited the highest DPPH and ABTS radical scavenging activities, suggesting a synergistic effect between trahanas-derived bioactive compounds and fermentation-associated lactic acid bacteria. Microbiological analyses confirmed the maintenance of high lactic acid bacterial populations throughout storage, particularly in the 4% trahanas formulation, which exhibited the highest Streptococcus thermophilus counts during refrigerated storage. The detected lactic acid bacterial populations originated both from the commercial yogurt starter culture and from the traditional preparation of trahanas itself, which involves fermentation with sour sheep’s milk and traditional yogurt. In addition, coliforms, Enterobacteriaceae, and Staphylococci remained undetectable in all formulations, while only limited yeast and mold growth was observed during the later stages of storage, mainly in starter-free samples. Sensory evaluation indicated good overall acceptability of trahanas-enriched formulations, particularly at 4% (w/w). Overall, the incorporation of traditional Greek trahanas into yogurt systems represents a promising approach for the development of fermented dairy products with improved technological, antioxidant-related, and functional properties.