Glucocorticoids are effective anti-inflammatory and immunosuppressive agents. Long-term exposure is associated with multiple metabolic side effects. Spore-forming probiotic bacteria have shown modulatory properties regarding glycolipid metabolism and inflammation. The aim of this study was to evaluate, for the first time, the effects of Bacillus species spores (B. licheniformis, B. indicus, B. subtilis, B. clausii, and B. coagulans) alone and in combination with metformin against dexamethasone-induced systemic disturbances. A total of 30 rats were randomly divided into 5 groups: group 1 served as control (CONTROL), group 2 received dexamethasone (DEXA), group 3 received DEXA and MegaSporeBiotic (MSB), group 4 received DEXA and metformin (MET), and group 5 received DEXA, MSB, and MET. On the last day of the experiment, blood samples and liver tissue samples for histopathological examination were collected. We determined serum glucose, total cholesterol, triglycerides, tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), interleukin-10 (IL-10), catalase, total antioxidant capacity (TAC), and metformin concentration. DEXA administration caused hyperglycemia and hyperlipidemia, increased inflammation cytokines, and decreased antioxidant markers. Treatment with MSB reduced total cholesterol, suggesting that the administration of Bacillus spores-based probiotics to DEXA-treated rats could ameliorate metabolic parameters.