A vegan diet has been associated with increased bone fracture risk, but the physiology linking nutritional exposure to bone metabolism has only been partially elucidated. This study investigated whether a vegan diet is associated with increased bone turnover and altered calcium homeostasis due to insufficient intake of calcium and vitamin D. Fractionated and total 25-hydroxyvitamin D (25(OH)-D), parathyroid hormone (PTH), calcium, and four bone turnover markers (osteocalcin, N-terminal propeptide of type I procollagen (PINP), bone-specific alkaline phosphatase (BAP), and C-terminal telopeptide of type I collagen (CTX)) were measured in serum from 78 vegans and 77 omnivores. When adjusting for seasonality and constitutional covariates (age, sex, and body fat percentage) vegans had higher concentrations of PINP (32 95% CI: 7, 64%, P = 0.01) and BAP (58 95% CI: 27, 97%, P < 0.001) compared to omnivores, whereas CTX (30 95% CI: -1, 72%, P = 0.06) and osteocalcin (21.8 95% CI: -9.3, 63.7%, P = 0.2) concentrations did not differ between the two groups. Vegans had higher serum PTH concentration (38 95% CI: 19, 60%; P < 0.001) and lower 25(OH)-D serum concentration (-33 95% CI: -45, -19%; P < 0.001), but similar serum calcium concentration (-1 95% CI: -3, 1%, P = 0.18 compared to omnivores. Vegans have higher levels of circulating bone turnover markers compared to omnivores, which may in the long-term lead to poorer bone health. Differences in dietary habits including intake of vitamin D and calcium may, at least partly, explain the observed differences.