OBJECTIVE To assess effects of 1-year Intelligent Physical Exercise Training (IPET) on musculoskeletal health. METHODS Office workers were randomized 1 : 1 to a training group, TG (N = 193), or a control group, CG (N = 194). TG received 1 h supervised high intensity IPET every week within working hours for 1 year and was recommended to perform 30 min of moderate intensity physical activity for 6 days a week during leisure. The IPET program was based on baseline health measures. RESULTS No baseline differences were present. An intention-to-treat analysis showed significant between-group effect for muscle strength but not for musculoskeletal pain. However, a per-protocol analysis of those with an adherence of ≥70% demonstrated a significant between-group effect for neck pain during the past three months. Several significant within-group changes were present, where TG and TG ≥ 70% demonstrated clinically relevant pain reductions whereas minimal reductions were seen for CG. CONCLUSIONS IPET and recommendations of moderate intensity physical activity demonstrated significant between-group effect on muscle strength. Interestingly, significant within-group reductions in musculoskeletal pain were seen not only in TG but also in CG. This may underlie the lack of such between-group effect and shows that a possible positive side effect of merely drawing attention can improve musculoskeletal health.