The purpose of this paper was to evaluate the effect of thermal treatment (TT: 121 ± 2 °C, 15 min) on the composition of commercial sweeteners diluted in water (10 °Brix). Additionally, we evaluated the impact of this TT on metabolic responses in C57BL/6 mice during a 24-week treatment. The sweeteners included in this study were sucrose (SC), glucose-63 (GLU63), agave syrup (AS), sucralose (SUC), and steviol glycosides (STG). HPLC analysis showed changes in the concentration of simple sugars of GLU63 and AS after TT. Importantly, in all sweeteners, TT modulated metabolic responses in mice. The mice drinking thermally treated sweetener solution showed an increase of 10−13% (p < 0.05) in food intake (AS, SUC, and STG), beverage intake (2−21%; SC and GLU63), weight gain (38%; SUC), energy (10−13%; AS, SUC, and STG), glucose levels (11−17%; SC and STG), GLP-1 (30%; SC) and insulin (88%; AS) release, and the generation of protein carbonyl (SC) and malondialdehyde (all sweeteners tested) compared to mice drinking solution without TT. In conclusion, TT of sweetener solutions accentuates the metabolic responses of healthy mice, which can be related to overweight and its comorbidities.