Background: Zinc has a critical role in metabolism and growth. This study aims to determine the effects of low-energy diets differing in macronutrient composition on zinc intake, estimated zinc bioavailability (phytate:zinc molar ratio) and plasma zinc concentration and associations between zinc status and cardiometabolic markers in obese adolescents with clinical insulin resistance (IR). Methods: Eighty-seven obese adolescents (10-17 years, body mass index z-score 2.3 ± 0.37) with clinical IR were randomized to a low-energy diet (6.0-8.0 MJ), which was either high carbohydrate or moderate carbohydrate with increased protein. Twenty-four-hour dietary recalls were collected at 6, 9 and 12 weeks. Plasma zinc concentration and cardiometabolic markers were assessed at baseline and 12 weeks. Results: Zinc intake did not differ between the 2 diet groups (p = 0.612). The high-carbohydrate group had a higher phytate intake (894 vs. 671 mg, p = 0.018) and phytate:zinc molar ratio (9.4 vs. 7.4, p = 0.009) than the increased-protein group. Plasma zinc concentration did not change from baseline in either of the diet groups, but correlated positively with zinc intake (r = 0.235, p = 0.042) and % energy from protein (r = 0.383, p = 0.001), and inversely with % energy from carbohydrate (r = -0.296, p = 0.010). Conclusions: Low energy diets for obese adolescents at risk of diabetes may need increased protein content to optimize zinc bioavailability.