Nowadays, agave syrup (AS) is a controversial sweetener due to its high fructose content. However, the hydrolysis process to which AS is subjected could contribute to improving its functional properties. This work aimed to evaluate the relationship between the degree of hydrolysis (DH) of AS (95%: AS95, 88%: AS88, and 50%: AS50) and its functional properties. In addition, the impact of these properties on weight gain, blood biochemical parameters, and oxidative stress (lipids and proteins) was studied in C57BL/6 mice. By HPLC analysis, the main polyphenols identified in AS were catechin, chlorogenic acid, caffeic acid, vanillin, quercetin, naringin, rutin, ellagic acid, and gallic acid. As the DH of AS increased, its fructose concentration increased (p < 0.05), and its concentration of fructans, bioactive compounds (BC), and antioxidant capacity decreased. In the case of blood glucose, the mice drinking AS solutions did not present differences (p > 0.05) in comparison to the control (water). However, mice drinking AS50 solutions showed a decrease (p < 0.05) in weight gain (35%), cholesterol (6%), triglycerides (18–22%), and oxidative stress in lipids (63%) and proteins (44%) compared to mice drinking AS88 and AS95 solutions.