Purpose <p>Coffee is a widely consumed source of bioactive compounds globally, yet its associations with circulating metabolites, sex hormones, and cardiometabolic markers remain incompletely characterised. We investigated these associations in a large population-based cohort, with particular attention to sex-specific hormonal profiles and metabolomic signatures.</p> Methods <p>Cross-sectional data from 2,264 participants (47% men) of the Northern Finland Birth Cohort 1966 (NFBC1966) at age 46 were analysed using sex-stratified Spearman correlations and multivariable linear regression models adjusted for BMI, educational attainment, smoking, physical activity, and alcohol intake.</p> Results <p>Higher coffee intake groups showed lower total and visceral fat and higher skeletal muscle mass, while BMI was comparable across groups. Inverse correlations were observed between coffee intake and circulating branched-chain amino acids (BCAAs) in both sexes. In men, higher coffee intake correlated with a more favourable glucose–insulin profile. Multivariable-adjusted models revealed a distinct hormonal pattern: positive associations with total testosterone (β = +0.29 nmol/L per cup/day), bioavailable testosterone, and sex hormone–binding globulin (SHBG), alongside inverse associations with free testosterone and the free androgen index (FAI). In women, hormonal associations were more limited, with positive associations for SHBG and inverse associations for free testosterone and FAI.</p> Conclusions <p>Higher habitual coffee intake groups showed a leaner body composition, correlated inversely with circulating BCAAs in both sexes, and were independently associated with a sex-specific hormonal profile that may be metabolically relevant, particularly in men. Future longitudinal and intervention studies are needed to establish causality and identify the coffee-derived bioactive compounds involved.</p>