Aim The purpose of this study was to examine whether the combination of high-intensity interval training (HIIT) and post-exercise protein supplementation would improve cardiovascular outcomes in individuals with T2D. Methods In a double-blind controlled trial, fifty-three adults with T2D (free of CVD and not on exogenous insulin) were randomized to 12 weeks of cardio and resistance-based HIIT (4-10 × 1 min at 90% maximal heart rate) with post-exercise milk, milk-protein, or placebo supplementation, thrice weekly. Before and after, carotid and femoral artery intima media thickness (IMT) and femoral flow profiles were assessed using high-resolution ultrasound. Central and peripheral arterial stiffness were assessed by pulse wave velocity (PWV), and resting and maximal heart rate rates were measured. Results After 12 weeks of HIIT femoral IMT (Pre: 0.84 ± 0.21 mm vs. Post: 0.81 ± 0.16 mm, p = 0.03), carotid-femoral PWV (Pre: 10.1 ± 3.2 m/s vs. Post: 8.6 ± 1.8 m/s, p < 0.01) and resting heart rate (Pre: 70.4 ± 10.8 bpm vs. Post: 67.8 ± 8.6 bpm, p = 0.01) were all significantly lower. There were no differences between nutrition groups (all significant main effects of time) for all outcomes. Conclusion HIIT reduces femoral IMT, arterial stiffness and resting heart rate in individuals with T2D. The addition of post-exercise milk or protein to HIIT did not have additive effects for improving cardiovascular outcomes in the present study. Taken together, HIIT alone may be an effective means to reduce the burden of cardiovascular complications in T2D.