Subjects with obesity and elevated fasting blood glucose are at high risk of developing type 2 diabetes which may be reduced by a dietary intervention leading to an improvement of insulin resistance. We investigated the potential of a whole-grain based dietary product (WG) with reduced starch content derived from double-fermented wheat during a hypo-energetic diet to positively influence body weight, fasting blood glucose, insulin resistance and lipids in comparison to a nutrient-dense meal replacement product (MR) in a randomized two-way cross-over study with two 4-week treatment periods separated by a 2-week wash-out. Subjects replaced at least two daily meals with WG and MR, respectively, targeting for a consumption of 200 g of either product per day. Total daily energy intake was limited to 7120 kJ. Thirty-one subjects (BMI 33.9 (SD 2.7) kg/m2, fasting blood glucose 6.3 (SD 0.8) mmol/l) completed the study. In both treatment groups body weight (-2.5 (SD 2.0) v. - 3.2 (SD 1.6) kg for WG v. MR), fasting blood glucose (-0.4 (SD 0.3) v. -0.5 (SD 0.5) mmol/l), total cholesterol (-0.5 (SD 0.5) v. -0.6 (SD 0.5) mmol/l), TAG (-0.3 (SD 0.9) v. -0.3 (SD 1.2) mmol/l) and homeostasis model assessment (HOMA) insulin resistance score (-0.7 (SD 0.8) v. -1.1 (SD 1.7) microU/ml x mmol/l) improved (P < 0.05) with no significant differences between the treatments. After statistical adjustment for the amount of body weight lost, however, the comparison between both groups revealed that fasting serum insulin (P = 0.031) and HOMA insulin resistance score (P = 0.049) improved better with WG than with MR. We conclude that WG favourably influences metabolic risk factors for type 2 diabetes independent from the amount of body weight lost during a hypo-energetic diet.