Purpose Diabetes Mellitus (DM) is a systemic disease that can effect tissues and their physiological functions at molecular and biochemical levels. Diabetic osteoporosis is one of the chronic diseases of bone metabolism effected by and characterized by augmented risk of osteoporotic fractures and destroying of bone microarchitecture. It was aimed to investigate the alterations in femoral bone structure that may take place as a complication of DM by using the antioxidant properties of eugenol and quercetin, which are phenolic compounds, in streptozotocin nicotinamide (STZ-NA) induced rats as an experimental type 2 DM (T2 DM) model. Methods The antioxidant effect of eugenol and quercetin in case of DM development was determined by GSH ELISA kit. The effect of DM on alterations in bone structure was analyzed by micro CT. BMD, Tb.Bv/Tb.Tv, Tb.N, Tb.Th, Ct.Th, Tb.Sp and SMI data were calculated with the software CTAn. Results Serum GSH levels, Tb.Th and Tb.Bv/Tb.Tv values statistically decreased, and SMI values statistically increased in diabetic group compared with controls. Serum GSH levels in eugenol group were higher than diabetic group, and Tb.Bv/Tb.Tv values in eugenol group were lower than controls. Quercetin group had higher serum GSH levels and Tb.Th values compared with diabetic group, while SMI values were lower in quercetin group compared with diabetic group. Conclusion Eugenol and quercetin were revealed to have antioxidant, antidiabetic and osteoprotective effects on the repair of bone structure in experimental STZ-NA T2 DM model.