Stenocereus queretaroensis fruits are endemic to Mexico. They have an excellent advantage in cultivation because they require little water and fertilizers. These plants do not require fungicides and herbicides, drastically reducing production costs. However, the nutritional contribution and potential health benefits of S. queretaroensis fruits are unknown. The physicochemical characterization, the content of bioactive compounds, and the antioxidant capacity (AOX) of four S. queretaroensis fruits (red, purple, yellow, and white) were evaluated. All fruits had a low sugar content (7.04–8.96%) and provided 4–5% dietary fiber. The purple and red fruits presented 19.7–20.29 mg/100 g fresh weight (fw) of total betalains, respectively, while the yellow fruit presented 9.21 mg/100 g fw of total carotenoids. The total soluble phenols were 54.86–62.14 mg/100 g fw. Flavonoids, hydroxycinnamic, and hydroxybenzoic acids were also found in all fruits in ascending order. The red fruit exhibited the highest AOX, followed by the yellow, purple, and white fruits. In conclusion, these fruits are a rich source of antioxidants and nutrients, highlighting that they provide 20% of daily consumption of dietary fiber and have a low caloric content. S. queretaroensis fruits, therefore, may have a high potential functionality, especially in people with diabetes and living with obesity.