It is known that mechanical loading leads to an increase in bone mass through a positive shift in the balance between bone formation and bone resorption. How the remodeling sites change over time as an effect of loading remains, however, to be clarified. The purpose of this paper was to investigate how bone formation and resorption sites are modulated by mechanical loading over time by using a new imaging technique that extracts three dimensional formation and resorption parameters from time-lapsed in vivo micro-computed tomography images. To induce load adaptation, the sixth caudal vertebra of C57BL/6 mice was cyclically loaded through pins in the adjacent vertebrae at either 8 N or 0 N (control) three times a week for 5 min (3000 cycles) over a total of 4 weeks. The results showed that mechanical loading significantly increased trabecular bone volume fraction by 20% (p < 0.001) and cortical area fraction by 6% (p < 0.001). The bone formation rate was on average 23% greater (p < 0.001) and the bone resorption rate was on average 25% smaller (p < 0.001) for the 8 N group than for the 0 N group. The increase in bone formation rate for the 8 N group was mostly an effect of a significantly increased surface of bone formation sites (on average 16%, p < 0.001), while the thickness of bone formation packages was less affected (on average 5% greater, p < 0.05). At the same time the surface of bone resorption sites was significantly reduced (on average 15%, p < 0.001), while the depth of resorption pits remained the same. For the 8 N group, the strength of the whole bone increased significantly by 24% (p < 0.001) over the loading period, while the strain energy density in the trabecular bone decreased significantly by 24% (p < 0.001). In conclusion, mouse tail vertebrae adapt to mechanical loading by increasing the surface of formation sites and decreasing the surface of resorption sites, leading to an overall increase in bone strength. This new imaging technique will provide opportunities to investigate in vivo bone remodeling in the context of disease and treatment options, with the added value that both bone formation and bone resorption parameters can be nondestructively calculated over time.