Fructose, a widely used sweetener in food and pharmaceutical industries, is linked to alterations in gut microbiota, bacterial metabolic changes, and chronic diseases. Therefore, functional buttermilk (FB) supplemented with 5% Red Beetroot Juice (RBJ), microencapsulated Lacticaseibacillus paracasei subsp. paracasei B-4564 and/or Bifidobacterium bifidum B-41410 were developed as a dietary intervention against High-Fructose Corn Syrup (HFCS) disorders in rats. Results revealed that RBJ exhibited potent antioxidant activity, 69.11% and 78.91% according to DPPH and ABTS assays, respectively. Higher survival rate and excellent stability of microencapsulated L. paracasei B-4564 and B. bifidum B-41410, either individually or in combination form, were observed during the storage period. Counts of microencapsulated probiotics increased significantly, L. paracasei B-4564 counts reached 9.60 and 9.75 log₁₀ CFU/ml in T1 (FBRP) and T3 (FBRM), whereas B. bifidum B-41410 reached 9.46 and 9.55 log₁₀ CFU/ml in T2 (FBRB) and T3 (FBRM), respectively. Additionally, after 5 months of in vivo study, biochemical parameters, fecal microbial counts, and histopathological examination of liver & intestinal tissues were evaluated. FBRM showed the most improvements in metabolic markers, including glucose, IR, liver functions, and lipid profiles, compared to the other groups. Significant reduction of rats' fecal coliforms was found in contrast with the promotion of probiotic counts. Histopathological evaluation showed marked improvements to intestinal & liver tissues of rats receiving FBRM, followed by FBRP and FBRB, compared to the positive control. It could be recommended that daily administration of functional buttermilk supplemented with 5% RBJ and mixed microencapsulated L. paracasei B-4564 and B. bifidum B-41410 is an effective tool to overcome pathological features contributed to HFCS consumption.