Critical care physicians are commonly faced with patients exhibiting atrial fibrillation (AF), a cardiac arrhythmia with multifaceted origins. Recent investigations shed light on the heterogeneity among AF patients by uncovering unique AF phenotypes, characterized by differing treatment strategies and clinical outcomes. In this retrospective study encompassing 9401 AF patients in an intensive care cohort, we sought to identify differences in average treatment effects (ATEs) across different patient groups. We extract data from the MIMIC-III database, use hierarchical agglomerative clustering to identify patients’ phenotypes, and assign them to treatment groups based on their initial drug administration during AF episodes. The treatment options examined included beta blockers (BBs), potassium channel blockers (PCBs), calcium channel blockers (CCBs), and magnesium sulfate (MgS). Utilizing multiple imputation and inverse probability of treatment weighting, we estimate ATEs related to rhythm control, rate control, and mortality, approximated as hourly and daily rates (%/h, %/d). Our analysis unveiled four distinctive AF phenotypes: (1) postoperative hypertensive, (2) non-cardiovascular mutlimorbid, (3) cardiovascular multimorbid, and (4) valvulopathy atrial dilation. PCBs showed the highest cardioversion rates across phenotypes, ranging from 11.6%/h (9.35–13.3) to 7.69%/h (5.80–9.22). While CCBs demonstrated the highest effectiveness in controlling ventricular rates within the overall patient cohort, PCBs and MgS outperformed them in specific phenotypes. PCBs exhibited the most favorable mortality outcomes overall, except for the non-cardiovascular multimorbid cluster, where BBs displayed a lower mortality rate of 1.33%/d [1.04–1.93] compared to PCBs’ 1.68%/d [1.10–2.24]. The results of this study underscore the significant diversity in ATEs among individuals with AF and suggest that phenotype-based classification could be a valuable tool for physicians, providing personalized insights to inform clinical decision making.