This study characterized bone structure, composition, and mechanical properties in growing male mice. The development of the collagen network during maturation was monitored, and the effect of voluntary physical exercise was investigated. We hypothesized that increased bone loading from exercise would increase the amount and improve the properties of the collagen network during growth and maturation. Half of the mice (total n = 168) had access to running wheels, while half were kept sedentary. Weight and running activity were recorded, and groups of mice were killed at 1, 2, 4, and 6 months of age. The collagen network was assessed by biochemical evaluation of collagen content and cross-links and by tensile testing of decalcified bone. Mineralized femur was analyzed with pQCT and three-point-bending and femoral neck-strength tests. After 6 months, the exercising mice had 10% lower body weight than the sedentary group. There was no difference in the amount of collagen or collagen cross-links, while tensile testing had higher breaking force and stiffness of the collagen network in runners after 4 months but not after 6 months. The bone mineral density and cross-sectional area were higher in the running group after 6 months. Runners also showed higher breaking force and stiffness of the diaphysis and the femoral neck at 2 and 6 months. The significant modulation of mechanical properties of the collagen network without any change in collagen content indicates that physical exercise improves properties of the collagen network in maturing bone. The improvement after exercise of the properties of mineralized bone appears to be more pronounced and long-lasting compared to the early improved properties of the collagen network.