Bariatric surgery has become the best treatment for morbid obesity. It has been documented that it achieves higher remission rates of the associated comorbidities when compared with medical treatment. Our objective with this review is provide information about the remission rates of such metabolic alterations with an emphasis on type 2 diabetes mellitus (T2DM), and mainly about how the research on the mechanisms that explain these results have evolved. Initially, the remission mechanisms of conditions such as T2DM were focused on studying the immediate as well as long-term changes of glucose metabolism and the physiology of incretins and hormones of the appetite-satiety axis, concluding that early changes were weight independent and that chronic changes were consequential to sustained weight loss. The possibility of obtaining tissues during the surgery has incorporated the histological, functional, molecular, and genetic study of biopsies from the liver, subcutaneous, and visceral adipose tissue, among others. These new approaches have been combined with methods based on systems biology, to integrate the genetics, transcriptomics, metabolomics, and microbiota with the histological, functional, and molecular findings and their relationship with clinical outcomes. This will likely combine bariatric surgery with precision medicine, favoring a better selection of patients and a more accurate prediction of outcomes.