Key points Staphylococcus aureus showed a significant increase in relative abundance in CRSwNP patients following endoscopic sinus surgery compared to pre‐surgery samples. Other Staphylococcus species were found to correlate positively with S. aureus in patients with nasal polyps; among those, S. caprae correlated strongly while being the most represented in samples. Patients with recurrent nasal polyp growth exhibited a substantially greater postoperative increase in the relative abundance of S. aureus .