One of the key determinants of adult skeletal health is the maximization of bone mass during the growth period. Physical activity (PA) in combination with lean mass and fat mass contribute to a great extent to bone mineral accrual; however, PA changes significantly during puberty. The aim of the present study was to examine PA exposure relative to bone mass acquisition during a longer observation period. Daily PA was measured with 7-day accelerometry and bone mineral parameters by DXA in 11- to 13-year-old peripubertal boys (n = 169). Similar testing was done after 1 calendar year. Changes in sedentary time were negatively related to changes in whole-body bone mineral density (BMD), lumbar spine bone mineral content (BMC), lumbar spine bone area (BA), femoral neck (FN) BMD, and FN BMC (r > -0.157; p < 0.05). Sedentary time emerged as the main PA level in predicting changes in FN BMC (p = 0.027) and in combination with vigorous PA predicting changes in FN BMD (p < 0.024). In addition to the effect of body composition on the skeleton, increase in sedentary time emerged as one main physical activity predictor (in addition to vigorous PA) of bone mineral acquisition during a 12-month period in peripubertal boys.