Preserving and valorising Apulian food biodiversity is a key strategy to promote the innovation of agro-food systems associated with regional Marginal Areas, including a diverse range of animals, plants, and micro-organisms (especially those of interest for food fermentation). ‘Gentile di Puglia’’ is an autochthonous sheep breed of millenary origins typical of the South of Italy, particularly associated with Foggia province (i.e., Subappennino Dauno and Tavoliere areas), also recognised for its traditional cheese production. Here, we report a case study related to the marginal area of the Subappennino Dauno/Monti Dauni, in the north of the Apulian Region, i) isolating lactic acid bacteria (LAB) from sheep milk (breed ‘Gentile di Puglia’) and ii) performing a polyphasic characterisation of LAB for the design of a multi-strain starter culture for Pecorino cheese and the design of a cross-over cereal-based fermented beverage (‘Senatore Cappelli’ durum wheat variety). Regarding the characterisation of Pecorino cheese and wheat beverages, the experimental plan included evaluating the pH of the final product, conducting a sensory analysis, investigating volatilomics, antioxidant properties, total phenol content, and rheological properties, and assessing the growth of lactic acid bacteria in the final product. The evaluations concerned protechnological properties, antimicrobial activity, sensorial aspects, and the study of volatile organic compounds. An interesting protechnological variability among the different strains analysed was detected, highlighting the modulation of several of the properties of interest in the context of the crossover between the dairy and plant-based sectors. Mixed strains in Pecorino cheese was found interesting for several of the tested characterisation criteria, supporting the design of a mixed starter culture. 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 project. FB and MP received funding PNRR, Investment 1.3-Award Number: Project code PE00000003, Project: ONFOODS.