Sacha Inchi oil (SIO) and hybrid palm oil (HPO) are potential sources of unsaturated fatty acids to improve the lipid profile of dairy products. This study evaluated, for the first time, the effects of the daily consumption of yogurts with enhanced fatty acid profiles on plasma lipids related to cardiovascular disease (CVD) risk factors. A pilot, randomized, double-blind, parallel-controlled trial was conducted with 47 participants assigned to three groups: SIO-enriched yogurt (Group A), HPO-enriched yogurt (Group B), and plain yogurt (Group C). Fasting blood samples were collected at baseline and after 1, 2, and 3 months to measure plasma lipids (TC, LDL-C, HDL-C, and TAG), ApoA1, and ApoB. While no significant changes were observed in the overall lipid profiles, notable within-group effects were identified. The total cholesterol (TC) dropped by 2.8%, 1.3%, and 3.3%, and LDL-C by 1.6%, 2.5%, and 2% in Groups A, B, and C, respectively. Additionally, the intake of monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), and vitamin E significantly increased in Groups A and B. These results suggest that SIO and HPO can be used as milk fat substitutes to enhance the nutritional profile of yogurts without affecting CVD biomarkers in healthy individuals.