High-sugar diet-induced prediabetes and obesity are a global current problem that can be the result of glucose or fructose. However, a head-to-head comparison between both sugars on health impact is still lacking, and dfa1 has never been tested, and has recently been isolated from healthy volunteers. The mice were administered with the high glucose or fructose preparation in standard mouse chaw with or without dfa1 gavage, on alternate days, and in vitro experiments were performed using enterocyte cell lines (Caco2) and hepatocytes (HepG2). After 12 weeks of experiments, both glucose and fructose induced a similar severity of obesity (weight gain, lipid profiles, and fat deposition at several sites) and prediabetes condition (fasting glucose, insulin, oral glucose tolerance test, and Homeostatic Model Assessment for Insulin Resistance (HOMA score)). However, fructose administration induced more severe liver damage (serum alanine transaminase, liver weight, histology score, fat components, and oxidative stress) than the glucose group, while glucose caused more prominent intestinal permeability damage (FITC-dextran assay) and serum cytokines (TNF-α, IL-6, and IL-10) compared to the fructose group. Interestingly, all of these parameters were attenuated by dfa1 administration. Because there was a subtle change in the analysis of the fecal microbiome of mice with glucose or fructose administration compared to control mice, the probiotics altered only some microbiome parameters (Chao1 and abundance). For in vitro experiments, glucose induced more damage to high-dose lipopolysaccharide (LPS) (1 µg/mL) to enterocytes (Caco2 cell) than fructose, as indicated by transepithelial electrical resistance (TEER), supernatant cytokines (TNF-α and IL-8), and glycolysis capacity (by extracellular flux analysis). Meanwhile, both glucose and fructose similarly facilitated LPS injury in hepatocytes (HepG2 cell) as evaluated by supernatant cytokines (TNF-α, IL-6, and IL-10) and extracellular flux analysis. In conclusion, glucose possibly induced a more severe intestinal injury (perhaps due to LPS-glucose synergy) and fructose caused a more prominent liver injury (possibly due to liver fructose metabolism), despite a similar effect on obesity and prediabetes. Prevention of obesity and prediabetes with probiotics was encouraged.