Atrial fibrillation (AF) and concomitant cardiometabolic disease processes interact and combine to lead to adverse events, such as stroke, heart failure, myocardial infarction, and cardiovascular death. Circulating biomolecules provide quantifiable proxies for cardiometabolic disease processes. The aim of this study was to test whether biomolecule combinations can define phenotypes in patients with AF. This pre-specified analysis of the EAST-AFNET 4 biomolecule study assigned patients to clusters using polytomous variable latent-class analysis based on baseline concentrations of 13 precisely quantified biomolecules potentially reflecting ageing, cardiac fibrosis, metabolic dysfunction, oxidative stress, cardiac load, endothelial dysfunction, and inflammation. In each cluster, rates of cardiovascular death, stroke, or hospitalization for heart failure or acute coronary syndrome, the primary outcome of EAST-AFNET 4, were calculated and compared between clusters over median 5.1 years follow-up. Findings were independently validated in a prospective cohort of 748 patients with AF (BBC-AF; median follow-up 2.9 years). Unsupervised biomolecule analysis assigned 1586 patients (71 years old, 46% women) into four clusters. The highest risk cluster was dominated by elevated bone morphogenetic protein 10, insulin-like growth factor–binding protein 7, N-terminal pro-B-type natriuretic peptide, angiopoietin 2, and growth differentiation factor 15. Patients in the lowest risk cluster showed low concentrations of these biomolecules. Two intermediate-risk clusters differed by high or low concentrations of C-reactive protein, interleukin-6, and D-dimer. Patients in the highest risk cluster had a five-fold higher cardiovascular event rate than patients in the low-risk cluster. Early rhythm control was effective across clusters (Pinteraction = 0.63). Sensitivity analyses and external validation in BBC-AF replicated clusters and risk gradients. Biomolecule concentrations identify cardiometabolic subphenotypes in patients with AF at high and low cardiovascular risk. The quantification of 13 biomolecules pre-selected for their ability to provide quantitative proxies for cardiovascular disease processes assigns patients with recently diagnosed atrial fibrillation and comorbidities to four clusters. The main biomolecules contributing to the clustering process are N-terminal pro-B-type natriuretic peptide, insulin-like growth factor–binding protein 7, bone morphogenetic protein 10, angiopoietin 2, growth differentiation factor 15, interleukin-6, and C-reactive protein. These biomolecules explain 66–85% of the assignment to a cluster. The four clusters differ in their risk of cardiovascular events (cardiovascular death, stroke, or unplanned hospitalisation for heart failure or acute coronary syndrome) over a 5-year time horizon. Early rhythm control therapy is effective in all four clusters (Pinteraction = 0.63). The clusters and their associated risk are replicated in an independent cohort.