The beneficial effects of probiotics on human health have been extensively studied. Strains of Lactobacillus and Bifidobacterium have gained considerable attention, as they are major groups of probiotic bacteria that improve gastrointestinal health. Recently, probiotics have been found to have positive effects on obesity and type 2 diabetes mellitus (T2D) that go beyond the improvement of gut health. Probiotics can alter the secretion of substances such as leptin and adiponectin from white adipose tissue via certain mechanisms. Additionally, probiotics can modulate the adaptive immune system against low-grade inflammation caused by obesity. The potential role of probiotics in the treatment of T2D has garnered interest because of increasing evidence of the anti-diabetic effect of probiotics. In this review, we discuss the results of in vivo studies that have examined the use of probiotics to prevent obesity and T2D, while primarily focusing on the studies that explore the cellular and molecular mechanisms underlying the activity of promising probiotic strains. The conclusions of this review could be of help to researchers who are investigating the effects of probiotics on obesity or T2D, and to patients with these diseases.