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Vitamin D might play a role in metabolic processes and obesity. We therefore examined vitamin D effects on metabolic markers and obesity in a randomized controlled trial (RCT). This is a post-hoc analysis of the Graz Vitamin D&amp;TT-RCT, a single-center, double-blind, randomized placebo-controlled trial. We included 200 healthy men with serum 25-hydroxyvitamin D (25(OH) D) levels &lt;75 nmol/L. Subjects received 20,000 IU of vitamin D3/week (<i>n</i> = 100) or placebo (<i>n</i> = 100) for 12 weeks. Outcome measures were metabolic markers, anthropometric measures, and body composition assessed by Dual-energy X-ray absorptiometry. One-hundred and ninety-two men completed the study. We found a significant treatment effect on fasting glucose/fasting insulin ratio (−5.3 (−10.4 to −0.2), <i>p</i> = 0.040), whereas we observed no significant effect on the remaining outcome parameters. In subgroup analyses of men with baseline 25(OH)D levels &lt;50 nmol/L (<i>n</i> = 80), we found a significant effect on waist circumference (1.6 (0.3 to 2.9) cm, <i>p</i> = 0.012), waist-to-hip ratio (0.019 (0.002 to 0.036), <i>p</i> = 0.031), total body fat (0.029 (0.004 to 0.055) %, <i>p</i> = 0.026), and android fat (1.18 (0.11 to 2.26) %, <i>p</i> = 0.010). In middle-aged healthy men, vitamin D treatment had a negative effect on insulin sensitivity. In vitamin D deficient men, vitamin D has an unfavorable effect on central obesity and body composition.