“Paški sir” is produced on the island of Pag using milk from native Pag sheep. This study illustrates the impact of innovative production technologies on the aromatic profile of “Paški sir” cheese. The aroma profile of „Paški sir” cheese samples were analyzed using a gas chromatography-mass spectrometry method (GC-MS). A total of 136 components were detected in the cheese samples, including hydrocarbons (30), ketones (17), aldehydes (14), alcohols (30), esters (18), acids (19), and lactones (8). Cheeses produced using natural commercial rennet and commercial thermophilic dairy cultures (control group) contained the highest concentrations of ketones, alcohols, and lactones. Cheeses produced with lyophilized autochthonous lamb rennet and microencapsulated dairy cultures (group 1) contained the highest concentrations of hydrocarbons, while cheeses produced using innovative microcapsules based on autochthonous lamb rennet and dairy cultures (group 2) contained the highest concentrations of aldehydes, esters, and acids. The application of these innovative technologies in the preparation of autochthonous rennet and dairy cultures for use in traditional cheese production can enhance its recognition and demand in the global market without negatively altering the sensory properties of the cheese.