Short-term animal experiments and association studies in humans have shown that cola intake may have a detrimental impact on bone mineral density (BMD); however, other bone parameters have not been investigated. This study examined the effects of long-term cola consumption on the femoral bone microstructure using adult mice (n = 32) as an animal model, which were divided into water and cola groups depending on whether they received water or cola along with a standard rodent diet for 6 months. Micro-computed tomography revealed that cola intake did not significantly affect all measured parameters characterizing trabecular bone mass and microarchitecture, as well as cortical microarchitecture and geometry in both sexes, although a slight deterioration of these parameters was noted. Cola consumption also resulted in a slightly, statistically insignificant worsening of bone mechanical properties. In contrast to female mice, males receiving cola had a lower area of primary osteons’ vascular canals. Nevertheless, long-term cola intake did not cause evident pathological alterations in the femur of adult mice, possibly due to a balanced diet and no restriction of physical activity. Therefore, the adverse effects of cola consumption on BMD, the only bone parameter studied so far, may be caused by other risk and lifestyle factors.