A high-caloric intake combined with a sedentary lifestyle is an important player in the development of type 2 diabetes mellitus (T2DM). The present study was undertaken to examine if the level of physical activity has impact on the metabolic effects of a high-caloric (+2,000 kcal/day) intake. Therefore, healthy individuals on a high caloric intake were randomized to either 10,000 or 1,500 steps per day for 14 days. Step-number, total energy expenditure, dietary records, neuropsychological tests, maximal oxygen uptake (VO2max), whole body dual-energy X-ray absorptiometry (DXA)- and abdominal magnetic resonance imaging (MRI)- scans, continuous glucose monitoring (CGM), and oral glucose tolerance tests (OGTT) with stable isotopes were performed before and after the intervention. Both study groups gained the same amount of body weight. However, the inactive group accumulated significantly more visceral fat compared to the active group. Following the two-week period, the inactive group also experienced a poorer glycaemic control, increased endogenous glucose production, decreased hepatic insulin extraction, increased baseline plasma levels of total cholesterol and LDL, and a decreased cognitive function with regard to capacity of attention. In conclusion, we find evidence to support that habitual physical activity may prevent pathophysiological symptoms associated with diet-induced obesity.