Safeguarding Apulian agro-biodiversity is of interest in driving bio-based innovation within the food systems of regional marginal territories. The 'Gentile di Puglia' sheep breed, a long-standing local variety from Southern Italy and especially the Foggia province, is closely linked to traditional dairy practices and local transhumance phenomena. In this study, we focused on the Subappennino Dauno region in northern Apulia, where we isolated lactic acid bacteria (LAB) from the milk of this indigenous breed. A comprehensive, polyphasic approach was employed to characterize these LAB strains in order to formulate multifunctional starter cultures suitable for Pecorino cheese manufacturing and for fermenting a cereal-based beverage using the ‘Senatore Cappelli’ durum wheat variety. The investigation covered technological features, antimicrobial efficacy, sensory profiles, and the production of volatile organic compounds. Fermentation and fermented products represent interesting elements to ensure the transition of food systems toward marginal areas sustainability. MF, HC, GS and VC are supported by the funding of the European Union Next-Generation EU [PNRR—Mission 4 Component 2, Investment 1.4—D.D. 1032 17/06/2022, CN00000022] within the Agritech National Research Centre for Agricultural Technologies. FB and MP, under the same scheme, Investment 1.3 - PE00000003, title: “ON Foods-Research and innovation network on food and nutrition Sustainability, Safety and Security—Working ON Foods”.