We found that the fasted metabolome of T2DM participants still differed from healthy control subjects after the exercise intervention, with metabolites such as (branched‐chain) amino acids, VLDL triglycerides, cholesterol and phospholipids, apolipoprotein B100/apolipoprotein A1 ratio and glycoprotein signals GlycA and GlycB being elevated, but HDL phospholipids, SPC2 and SPC3 being decreased in people with T2DM when contrasted with healthy control subjects. Here, PCSK2 is linked to type 2 diabetes mellitus.