Prospective inter-relationships among biomarkers were unexplored, which may provide mechanistic insights into diseases. We investigated the longitudinal associations of BMI change with trajectories of biomarkers related to cardiometabolic or breast cancer risk. A longitudinal study was conducted among 444 healthy women between 2019 to 2021. Cross‑lagged path analysis was used to examine the temporal relationships among BMI, cardiometabolic risk score (CRS), and obesity‑related proteins score (OPS) of breast cancer. Linear mixed-effect models were applied to investigate associations of time-varying BMI with biomarker-based risk score trajectories. Baseline BMI was associated with subsequent change of breast cancer predictors (P = 0.03), and baseline CRS were positively associated with OPS change (P < 0.001) but not vice versa. After fully adjustment of confounders, we found a 0.058 (95%CI = 0.009-0.107, P = 0.020) units increase of CRS and a 1.021 (95%CI = 0.041-1.995, P = 0.040) units increase of OPS as BMI increased 1 kg/m2 per year in postmenopausal women. OPS increased 0.784 (95%CI = 0.053-1.512, P = 0.035) units as CRS increased 1 unit per year. However, among premenopausal women, BMI only significantly affected CRS (β = 0.057, 95%CI = 0.007 to 0.107, P = 0.025). No significant change of OPS with time-varying CRS was found. Higher increase rates of BMI were associated with worse trajectories of biomarker-based risk of cardiometabolic and breast cancer. The longitudinal impact of CRS on OPS is unidirectional. Recommendations such as weight control for the reduction of cardiometabolic risk factors may benefit breast cancer prevention, especially in postmenopausal women.© 2023. The Author(s).