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Background: Impaired bone health is a recognized complication of type 1 diabetes. This study evaluated the effects of low-carbohydrate (LC) and Mediterranean (MED) diets on bone turnover markers in adolescents and young adults. Methods: In a 24-week randomized controlled trial, 40 individuals aged 12-21 years, with type 1 diabetes, were assigned to an LC or MED intervention (20 participants per group). C-terminal telopeptide (CTX) and procollagen type 1 N-terminal propeptide (P1NP) were measured at baseline and 24 weeks. Results: The groups had similar baselines. At 24 weeks, the between-group difference in delta glucose time in range was not statistically significant; median daily carbohydrate intake was 86 g (68-95) in LC and 130 g (102-173) in MED (p < 0.001). Comparing LC to MED, the median BMI z-score was lower (-0.1 [-0.3 to -0.1] vs. 0.0 [-0.1 to -0.1], p = 0.10), and calcium (p = 0.035) and magnesium intakes (p = 0.030) were lower. These associations did not remain statistically significant after false-discovery-rate correction. The median-adjusted alkaline phosphatase level decreased significantly in the LC group (p = 0.009). The median CTX changed following LC from 395 pg/mL (232-591) to 423 pg/mL (289-591) (p = 0.278); and following MED, from 357 pg/mL (244-782) to 296 pg/mL (227-661) (p = 0.245). P1NP changed in LC from 95 ng/mL (68-112) to 88 ng/mL (62-97) (p = 0.056) and in MED from 76 ng/mL (54-198) to 71 ng/mL (55-122) (p = 0.594). Conclusions: Exploratory analyses of bone turnover markers showed insignificant differences following LC and MED diets.