Physical activity questionnaires utilised in research generally assess metabolic equivalents of task (METs). It is unclear whether mechanical loading during physical activity, estimated from METs-based questionnaires, is associated with skeletal health. This cross-sectional study investigated how physical activity of high loading intensities and rates, assessed at ages 17- and 20-years, (a) compares with physical activity measured in METs, and (b) is associated with bone mass at age 20 years. 826 participants from the Raine Study Gen2 were assessed for physical activity energy expenditure over the past week via the International Physical Activity Questionnaire (IPAQ) at age 17- and 20-years. Loading scores (the product of peak force and application rate of an activity) per week were subsequently estimated from the IPAQ. Whole-body and appendicular bone mineral density (BMD) at age 20-years were assessed by dual-energy X-ray absorptiometry. Bland-Altman minimal detectable difference for physical activity Z-scores at age 17- and 20-years were 1.59 standard deviations (SDs) and 1.33 SDs respectively; greater than the a priori minimal clinically important change of 0.5 SDs. Loading score at age 17- and 20-years, but not IPAQ score, had significant positive associations with whole-body and leg BMD after adjustment for covariates (β=0.008 and 0.012g/cm2 respectively). IPAQ score at age 20-years, but not loading score, had a significant positive association with arm BMD (β=0.007g/cm2). There was no significant association between 3-year change in IPAQ or loading score and bone mass. This study revealed disagreement in associations of self-reported METs and loading score estimates with bone health in young adults. Participation in physical activity with higher loading scores was associated with whole-body and leg BMD, while higher energy expenditure was associated with arm BMD. Coupling traditional energy expenditure questionnaire outcomes with bone-loading estimates may improve understanding of the location-specific skeletal benefits of physical activity in young adults.