Background and objectives: genetic variants of the APOA1 gene have been related to lipid profile in obese subjects. Our aim was to analyze the effects of the rs670 APOA1 gene polymorphism on metabolic changes secondary to an enriched-polyunsaturated fat vs. an enriched-monounsaturated fat hypocaloric diet. Methods: 360 Caucasian obese subjects were randomly allocated to two groups. One group received an enriched-polyunsaturated fat (diet P) and the other an enriched-monounsaturated fat hypocaloric diet (diet M) during 12 weeks. The effects on serum biomarkers related to lipid and carbohydrate metabolism were evaluated before and after the dietary intervention. Results: after both diets, body mass index, weight, fat mass, waist circumference, systolic blood pressure, plasma leptin concentration, and waist circumference decreased in all patients. After 12 weeks of intervention with diet P, plasma insulin levels and HOMA-IR decreased in A-allele carriers: delta: -7.3 ± 2.2 IU/L (p = 0.01), and delta: -2.8 ± 0.5 units (p = 0.02), respectively. The same changes in delta were observed after diet M in A-allele carriers: insulin delta: -5.9 ± 1.2 IU/L (p = 0.01), and HOMA-IR delta: -2.1 ± 0.8 units (p = 0.02). In A-allele carriers, LDL-cholesterol decreased and HDL-cholesterol increased after the dietary intervention with diet P: delta: -12.1 ± 4.3 mg/dL (p = 0.01), and delta: 2.6 ± 0.7 mg/dL (p = 0.01), respectively. No differences in lipid profile were observed after diet M. These improvements were not observed in non-A-allele carriers after both interventions. Conclusions: our study showed the association of the rs670 ApoA1 polymorphism with insulin resistance changes as induced by both diets. An enriched-polyunsaturated fat diet produced an additional improvement of HDL-cholesterol and LDL-cholesterol in A-allele carriers.