Abstract Aims Stent implantation during primary percutaneous coronary intervention (PCI) for ST-segment elevation myocardial infarction (STEMI) occasionally results in flow disturbances and distal embolization, which may cause adverse clinical outcomes. Deferred stent implantation seems to reduce the impairment on myocardial function, although the mechanisms have not been clarified. We sought to evaluate whether deferred stenting could reduce flow disturbance in patients treated with primary PCI. Methods and results Patients with STEMI included in the DANAMI-3-DEFER trial were randomized to deferred versus immediate stent implantation. The primary and secondary outcomes of this substudy were the incidences of slow/no reflow and distal embolization. A total of 1205 patients were included. Deferred stenting (n = 594) resulted in lower incidences of distal embolization [odds ratio (OR) 0.67, 95% confidence interval (CI) 0.46–0.98, P = 0.040] and slow/no reflow (OR 0.60, 95%CI 0.37–0.97, P = 0.039). In high-risk subgroups, the protective effect was greatest in patients >65 years of age (slow/no reflow: OR 0.36, 95% CI 0.17–0.72, P = 0.004 and distal embolization: OR 0.34, 95% CI 0.18–0.63, P = 0.001), in patients presenting with occluded culprit artery at admission (slow/no reflow: OR 0.33, 95% CI 0.16–0.65, P = 0.001 and distal embolization: OR 0.54, 95% CI 0.31–0.96, P = 0.036) and in patients with thrombus grade >3 (slow/no reflow: OR 0.37, 95% CI 0.20–0.67, P = 0.001 and distal embolization: OR 0.39, 95% CI 0.24–0.64, P < 0.001) with a significant P for interaction for all. Conclusion Deferred stent implantation reduces the incidences of slow/no reflow and distal embolization, especially in older patients and in those with total coronary occlusion or high level of thrombus burden.