Bioactive compounds have shown significant potential in the management of obesity and metabolic syndrome (MetS). This study investigates the effects of antioxidant lipids (ALω-3), synthetized through enzymatic acidolysis using non-specific lipase B from Candida antarctica under supercritical CO2 conditions. These lipids were derived from a concentrate of rainbow trout (Oncorhynchus mykiss) belly oil, rich in long-chain polyunsaturated omega-3 fatty acids (LCPUFAn-3), and cold-pressed maqui seed oil (MO, Aristotelia chilensis (Mol.) Stuntz). Their effects were then evaluated in a murine high-fat diet (HFD) model. The fatty acid profile, tocopherol and tocotrienol content, and thin-layer chromatography of ALω-3 were analyzed. After 8 weeks on an HFD, male C57BL/6 mice were divided into four groups and switched to a control diet (CD) with the following supplements for 3 weeks: Glycerol (G), commercial marine Omega-3 (CMω-3), a mixture of LCPUFAn-3 concentrate + MO (Mω-3), or ALω-3. The total body and organ weights, serum markers, and liver and visceral fat pro-inflammatory marker expression levels were assessed. ALω-3 contained 13.4% oleic, 33.9% linoleic, 6.3% α-linolenic, 10.7% eicosapentaenoic, and 16.2% docosahexaenoic fatty acids. The β, γ, δ-tocopherol, and β, γ-tocotrienol values were 22.9 ± 1.4, 24.9 ± 0.2, 6.8 ± 0.7, 22.9 ± 1.7, and 22.4 ± 4.7 mg·kg−1, respectively, with α-tocopherol detected in traces. ALω-3 supplementation increased serum Trolox equivalent capacity, significantly reduced serum GPT levels (p < 0.01), and enhanced postprandial glucose tolerance (p < 0.001), although it did not alter insulin resistance (HOMA-IR). These findings indicate ALω-3′s potential for mitigating the glucose intolerance, liver damage, and oxidative stress associated with obesity and MetS, highlighting the need for additional research to explore its potential health benefits.