Background: Due to the close association between gut microbiota and diabetes, probiotic dairy products draw a lot of attention in the development of functional foods with anti-diabetic activity. Methods: 28 type II diabetic patients twice a day received 10 grams of camel milk powder supplemented with BBA6 and camel milk powder (control) over a total of 4 weeks. Results: After the intervention, there was a significant decrease in fasting blood glucose, serum content of total cholesterol, the cardiovascular risk index (TC/HDL-C), the pro-inflammatory cytokines (IL-6, MCP-1) and adipokines (adiponectin, resistin, lipocalin-2, adipsin). Myokines (irisin, osteocrin) increased significantly, indicating possible improvement in skeletal muscle function. Gut microbiota analysis suggested a significant enrichment in unclassified_f__Sphingomonadaceae and depletion in Eggerthella after the 4-week intervention with the probiotic camel milk powder, there were also elevated fecal concentrations of elevated fecal concentrations of proline, uracil and galactinol accompanied with a decreased norleucine, glycerol, sedoheptulose, palmitic acid, 5-aminovaleric acid, inositol and γ-aminobutyric acid. Conclusion: Dietary supplement with 10 grams of probiotic camel milk powder twice a day for a consecutive 4 weeks can significantly decrease fasting blood glucose of type 2 diabetic patients. This functional food also improves dyslipidemia, inflammation and functions of adipocytes and skeletal muscle, indicating the possibility of probiotic camel milk powder as a dietary treatment that target metabolic syndrome such as diabetes. Trial registration: ClinicalTrials, NCT04296825, Registered 5th March 20206 - Retrospectively registered, https://www.clinicaltrials.gov/ct2/show/NCT04296825.