Objective: This study aimed to investigate the effect of exercise intensity on visceral adipose tissue (VAT) and liver fat reduction in patients with coronary artery disease (CAD) over 3 months and the maintenance of improvements over 12 months. Methods: Forty-two participants with CAD were randomized to three sessions/week of either 4 × 4-minute high-intensity interval training (HIIT) or 40 minutes of usual care moderate-intensity continuous training (MICT) for a 4-week supervised cardiac rehabilitation program, followed by three home-based sessions/week for 11 months. Liver fat (as intrahepatic lipid) and VAT were measured via magnetic resonance techniques. Data are mean change (95% CI). Results: HIIT and MICT significantly reduced VAT over 3 months (−350 [−548 to −153] cm3 vs. −456 [−634 to −278] cm3; time × group effect: P = 0.421), with further improvement over 12 months (−545 [−818 to −271] cm3 vs. −521 [−784 to −258] cm3; time × group effect: P = 0.577) and no differences between groups. Both groups improved liver fat over 3 months, with HIIT tending to show greater reduction than MICT (−2.8% [−4.0% to −1.6%] vs. −1.4% [−2.4% to −0.4%]; time × group effect: P = 0.077). After 12 months, improvements were maintained to a similar degree. Higher exercise intensity predicted liver fat reduction (β = −0.3 [−0.7 to 0.0]; P = 0.042). Conclusions: HIIT and MICT reduced VAT over 3 and 12 months. For liver fat, HIIT tended to provide a slightly greater reduction compared with MICT. These findings support HIIT as a beneficial adjunct or alternative to MICT for reducing visceral and liver fat in patients with CAD.