The present study aimed to investigate the effect of a dietary intervention including free or immobilized cells of the presumptive probiotic Pediococcus acidilactici ORE5 on Corinthian currants, a food with beneficial impact in the condition of Type-1 Diabetes Mellitus (T1DM), on the microbiome composition of STZ-induced diabetic rats. Twenty four male Wistar rats were divided into four groups (n = 6 per group): healthy animals, which received the free (H_FP) or the immobilized Pediococcus acidilactici ORE5 cells (H_IPC), and diabetic animals, which received the free (D_FP) or the immobilized Pediococcus acidilactici ORE5 cells(D_IPC) for 4 weeks (109 cfu/day, in all groups). At the end of the dietary intervention, the D_IPC group exerted a lower concentration of the inflammatory cytokine IL-1 beta compared to D_FP. Consumption of immobilized P. acidilactici ORE5 cells on Corinthian currants by diabetic animals led to increased loads of fecal lactobacilli and lower Enterobacteriaceae, coliforms, and Escherichia coli levels, while Actinobacteria phylum, Akkermansia, and Bifidobacterium genera abundances were increased, and fecal lactic acid was elevated. Overall, the results of the present research demonstrated that functional ingredients could ameliorate gut dysbiosis present in T1DM and could be used to design dietary patterns aiming at T1DM management. However, well-designed clinical trials are necessary, in order to confirm the beneficial effects in humans.