Abstract Background Adjunctive lung resection is recommended for selected patients with nontuberculous mycobacteria (NTM) pulmonary disease (PD). However, data on long-term recurrence rates in patients infected with major pathogens, including Mycobacterium avium complex (MAC) and Mycobacterium abscessus (MABC), are limited. Methods We retrospectively analyzed data from 125 patients with MAC-PD (n = 90) or MABC-PD (n = 35) who underwent adjunctive lung resection in a prospective observational study. We evaluated microbiological response, postoperative complications, recurrence, and all-cause mortality over a median 80-month follow-up. Results Persistent culture positivity (64%) was the most common indication for surgery, followed by hemoptysis, recurrent pneumonia, or radiologic deterioration. Postoperative complications occurred in 18 (14%) patients, with no surgery-related deaths. Treatment outcomes did not significantly differ between the MAC- and MABC-PD groups. Cure with culture conversion was achieved in 112 (90%) patients. Recurrence occurred in 37 (33%, 37/112) patients, of which 18 (49%, 18/37) were attributed to reinfection by different NTM species (or subspecies). MAC group had higher recurrence rates than the MABC group (Kaplan–Meier curve, log-rank test p = 0.043), and was significantly associated with recurrence in the multivariable analysis (adjusted hazard ratio, 2.71; 95% confidence interval, 1.23–5.99). However, mortality was higher in the MABC-PD group than in the MAC-PD group (7/35 vs. 4/90, p = 0.006). Conclusion Adjunctive lung resection with antibiotics helps reduce the bacterial burden and manage symptoms in patients with NTM-PD. However, it does not prevent recurrence, and recurrence is mostly caused by reinfection.