Introduction: Dairy products are an important source of antioxidant bioactive compounds. Fermentation with autochthonous lactic acid bacteria can enhance their functional properties while promoting the sustainable use of local microbial resources. Methods: Semi-cured raw goat milk cheeses were manufactured using five combinations of autochthonous strains of Lactococcus lactis and Leuconostoc mesenteroides (designated 1A, 1B, 2A, 2B, and 3A), together with a control cheese without starter culture. Proximate composition (moisture, protein, fat, ash, carbohydrates, and fatty acid profile) and antioxidant capacity were determined. Antioxidant activity was evaluated by TEAC and ORAC before and after in vitro gastrointestinal digestion (INFOGEST 2.0) to assess the effect of digestion on antioxidant potential. Results and Discussion: The incorporation of autochthonous lactic acid bacteria did not significantly alter the proximate composition of the cheeses or the overall fatty acid distribution (SFA, MUFA, and PUFA). However, fermentation selectively modulated minor fatty acids, reducing butyric acid (1.58–1.88 vs. 2.62% in the control) and increasing petroselinic acid (0.75–1.26 vs. 0.20%), cis-vaccenic acid (0.25–0.37 vs. 0.20%), and behenic acid (0.11–0.15%; not detected in the control). Simulated gastrointestinal digestion reduced antioxidant capacity by 87.7–94.9% (TEAC) and 90–94% (ORAC). Nevertheless, formulations 1B and 2A retained significantly higher TEAC values than the control (45.4 and 42.8 vs. 34.9 μmol TE/100 g DW, respectively), whereas formulation 1A showed a significantly higher ORAC value (562.2 vs. 494.1 μmol TE/100 g DW). Conclusions: Selected combinations of autochthonous lactic acid bacteria modulated the functional properties of goat cheese through modulation of bioactive fatty acids and antioxidant capacity. These findings support the further evaluation of these formulations in preclinical models and human studies to validate their potential for the prevention of oxidative stress-related diseases.