Abstract: Beef is considered an excellent source of high-quality protein and micronutrients. The high saturated fatty acid (SFA) composition of beef has been associated with cardiovascular diseases; however, this is a controversial issue because at present, no evidence has scientifically proven such an association. Wagyu cattle have been used as an option to generate high-quality fatty acids (FAs) in beef and have been crossed with local beef cattle (Wagyu-Cross). In Mexico, Wagyu-Cross is marketed assuming the same quality as purebred Wagyu meat without scientific support. This study aimed to determine whether the differences in the FA composition of Wagyu-Cross and commercial beef affected lipid metabolism in frequent consumers of beef. The study is a randomized, controlled, double-blinded phase IV clinical trial. Thirty-four volunteers completed treatments in which 120 g ground beef was consumed 3 days per week for 2 weeks. Volunteers were randomized to the “A” (commercial meat) or “B” (Wagyu-Cross meat) groups. The beef fat content was 87% higher, the SFA content was 2.3% lower, and the monounsaturated fatty acid (MUFA) C18:1 n-9 concentrations were higher in Wagyu-Cross beef than in commercial beef. The B group exhibited a significantly larger change from baseline in the serum lipid profile in total cholesterol (TC) (−4.7% versus +6.9%), low-density lipoprotein (LDL) (−4.1% versus +10.0%), nonhigh-density lipoprotein (non-HDL) (−6.1% versus +4.9%), and the ratio of three atherogenic indexes—TC/HDL (−3.5% versus +6.4%), LDL/HDL (−2.8% versus +14.6%), and non-HDL/HDL (−4.7% versus +9.3%)—than the A group. This result confirms that meat FA composition is a key point for redirecting cattle breeding strategies and promotes beef as a healthful protein source. Practical Application: Here, we found new evidence based on a clinical trial that beef with a favorable fatty acid composition (i.e., monounsaturated fatty acid and polyunsaturated fatty acid content) is a key factor in improving parameters associated with consumer health. This information will support the design of cattle breeding strategies as an option to promote beef consumption as a healthier protein source and create opportunities for the development of the functional food industry.