Abstract Background Microvascular obstruction (MVO) has been associated with a higher risk of cardiac remodelling and adverse events following ST-segment elevation myocardial infarction (STEMI). However, long-term prognostic implications of MVO in STEMI beyond five years of follow-up have not been assessed to date. Purpose To investigate the relation of MVO with all-cause mortality and recurrent ischemic events at long-term follow-up after STEMI. Methods This is a pooled analysis of three observational studies including 876 prospectively enrolled reperfused first STEMI patients, who underwent cardiac magnetic resonance imaging with late gadolinium enhancement, between 2003-2019, from four university medical centers in the Netherlands and Spain. Median follow-up duration was 6.3 (IQR 3.6-9.3) years. The primary outcome was all-cause mortality. The secondary outcome was a combined endpoint of all-cause mortality and recurrent ischemic events (i.e. myocardial infarction or stroke). We performed Cox regression analyses with a time-dependent covariate. Model 1 included correction for clinical covariates only, i.e. age, sex, smoking, diabetes mellitus, hypertension, and LAD culprit artery. Model 2 included imaging characteristics, i.e. infarct size and left ventricular ejection fraction, in addition to the clinical covariates. Results The study population consisted of 876 patients, mean age 59 years ± 12, 720 men (82%). MVO was present in 499 patients (58%). The presence of MVO was significantly associated with all-cause mortality up to six years post-STEMI, independent from clinical characteristics (Hazard Ratio [HR] 2.23, 95% CI 1.09-4.57, p=0.029), but not after six years post-STEMI (HR 0.98, 95% CI 0.45-2.12, p=0.958). Presence of MVO was not significantly associated with a combined endpoint of all-cause mortality and recurrent ischemic events before or after six years of follow-up (HR 1.27, 95% CI 0.81-1.99, p=0.294 and HR 0.68, 95% CI 0.35-1.31, p=0.244, respectively). All other traditional prognosticators, except age, also lacked predictive value at long-term follow-up beyond six years. Conclusions In STEMI patients, the presence of MVO by cardiac magnetic resonance imaging is associated with a more than two-fold higher risk of all-cause mortality up to six years after the index event. This relation seems to dissipate beyond this time period. Furthermore, presence of MVO was not associated with recurrent ischemic events at long-term follow-up post-STEMI.