Biochemical bone turnover markers (BTMs) provide important information on the diagnosis, therapy and monitoring of metabolic bone diseases. They are evident before measurable changes in bone mineral density (BMD) take place. A total of 35 adult Saudi patients (23 males; 12 females) with type 2 diabetes and diagnosed to be vitamin D deficient were recruited in this prospective study. Here we investigated the effects of gender, season, and vitamin D status on bone biochemical markers of bone remodeling. Anthropometry and blood samples were collected at different intervals. Metabolic parameters and bone biomarkers were measured routinely and by ELISA. Both males and females had a significant increase in their vitamin D status over time, but no significant changes in the bone biomarkers were observed in females. In males there was a significant increase in circulating levels of corrected calcium and OPN (p = 0.004 and 0.01 respectively) and a significant decrease in crosslaps (p = 0.005). In all subjects there was a modest but significant positive relationship between vitamin D status and OC (R = 0.34; p = 0.04). In conclusion, our study demonstrates that changes in bone remodeling markers are affected by season, gender, and possibly vitamin D status. This gender difference may well reflect the physiologic pathway responsible for the higher peak bone mass achieved in males compared to females.