The study aimed to determine the effect of manganese (Mn) exclusion from the dietary mineral mixture and the dietary replacement of the recommended level of MnCO3 with Mn2O3 nanoparticles (Mn2O3NPs) on the Mn biodistribution and the femur histology. Methods: The experiment was conducted on twenty seven Wistar rats divided into three groups (n = 9): a control group receiving the recommended level of Mn (65 mg/kg) in standard form (MnCO3); a manganese deficient group (Mn deprived from dietary mineral mixture), and a group receiving diet supplemented Mn2O3NPs (65 mg/kg) instead of MnCO3. During the 12-week experiment, a balance test was performed. After the experiment period, blood and femur were collected from sacrificed rats. The content of Mn in water, diet, urine, feces, plasma, and femur was measured. Results: In the Mn-deficient rats, a reduction in Mn intake and excretion, Mn retention index, and blood Mn level, but an increase in Mn digestibility index was noted. In rats supplemented with Mn2O3NPs, Mn intake and excretion and blood Mn levels were decreased, while Mn retention and digestibility indexes were increased. In both experimental groups, deterioration of femur morphology was noted, but these changes were more severe in the Mn-deficient group. Conclusions: The obtained research results indicate that manganese deficiency significantly disturbed the biodistribution of this element and led to the deterioration of the architecture and histological parameters of the femur, emphasizing the key role of manganese in maintaining bone homeostasis. It has also been shown that replacing MnCO3 with Mn2O3NPs allows the maintenance of the correct Mn level in the femur but causes unfavorable changes in its morphology