Fatty Acid Profile and Lipid Quality of Milk from Indigenous Greek Goat Breeds Reared Under Semi-Extensive Systems

Background/Objectives: Goat milk is an important source of bioactive lipids, but information on the fatty acid (FA) profiles of indigenous Greek goat breeds under semi-extensive management remains limited. This study aimed to compare the milk FA composition and lipid health indices of Capra prisca, Skopelos, and crossbred goats in Thessaly, Greece, and to evaluate the effect of organic versus conventional semi-extensive production systems. Methods: Thirty bulk-tank milk samples were collected during spring 2025 from eight herds, comprising Capra prisca (n = 10), Skopelos (n = 10), and crossbred goats (n = 10), with 15 samples from each production system. Physicochemical characteristics were determined using an ultrasonic milk analyzer, while FA composition was analyzed by gas chromatography with flame ionization detection (GC–FID). Lipid quality indices, including the Atherogenicity Index (AI) and Thrombogenicity Index (TI), were calculated. Statistical analyses were performed using two-way ANOVA with Benjamini–Hochberg adjustment. Results: Breed significantly affected several individual FAs but not total SFA, MUFA, or UFA concentrations. Capra prisca milk contained higher levels of C4:0, C18:0, and C18:3n6 (pBH ≤ 0.015), whereas Skopelos milk showed higher C16:0 and lower C18:2n6 isomers (pBH ≤ 0.046). Total PUFA and ω-6 concentrations were higher in Capra prisca and crossbred milk than in Skopelos milk (pBH ≤ 0.004). In contrast, total ω-3 concentrations and lipid health indices did not differ significantly among breeds or between production systems (AI = 2.5–2.7; TI = 3.0–3.3; PUFA/SFA = 0.06–0.07; pBH ≥ 0.192). Conclusions: Under semi-extensive management, breed was associated primarily with differences in individual FAs and total ω-6 PUFA concentrations, whereas overall lipid health indices were relatively stable. No significant differences were observed between organic and conventional production systems. These findings provide baseline information on the milk lipid composition of indigenous Greek goat breeds and support further investigation using larger, multi-season datasets.