Diabetes mellitus is a common endocrine disorder in dogs and cats, and achieving stabilization with insulin alone can be challenging. This study evaluated the glucose-lowering efficacy and safety of Bifidobacterium longum CKD1 in diabetic companion animals. Nine dogs and 13 cats received B. longum CKD1 daily for 12 weeks. Fasting blood glucose (FBG) levels decreased by 26.2% in dogs and 18.0% in cats. Remarkable improvement in FBG was observed in dogs and cats with baseline levels exceeding 200 mg/dL in dogs and 250 mg/dL in cats. Notably, dogs exhibited a significant 61.8% reduction (p < 0.05), while cats showed a 38.4% decrease. Insulin-treated cats required significantly lower insulin doses by Week 12 (p < 0.05). Continuous glucose monitoring in cats demonstrated a 21.6% reduction in mean glucose levels and a significant 32.3% decrease in the time spent with glucose levels above 181 mg/dL (p < 0.05). Microbiota analysis revealed an increase in beneficial commensals and short-chain fatty acid producers, along with a reduction in pathobionts. No treatment-related adverse effects were observed. These findings indicate that B. longum CKD1 improves glycemic control and safely modulates the gut microbiota, supporting its potential use in managing diabetes mellitus in companion animals.