Background: Pilonidal sinus disease (PSD) is a chronic inflammatory condition predominantly affecting young adults. Minimally invasive techniques such as pit-picking have gained increasing popularity; however, recurrence rates remain a significant concern. Microwave ablation (MWA) has recently emerged as a novel adjunctive modality that may improve treatment durability through enhanced destruction of residual sinus epithelium. Materials and Methods: This retrospective multicenter comparative cohort study included 403 consecutive patients treated for PSD between January 2022 and January 2024. Among these, 200 patients underwent pit-picking combined with MWA (MWA group) and 203 underwent pit-picking alone (PP group). Recurrence was defined as any clinical reappearance of pit, abscess, or discharging sinus confirmed at follow-up. Primary outcome was disease recurrence; secondary outcomes included operative time, postoperative pain (VAS), complications, SSI, wound healing time, pain-free sitting, and return to work. Multivariable logistic regression and Kaplan–Meier analysis were performed. Results: MWA group demonstrated superior postoperative outcomes: shorter pain-free sitting (2 vs 4 days), healing time (11 vs 16 days), and return to work (3 vs 5 days). Overall complication rates were lower (4.5% vs 11.3%; OR 0.37, 95% CI 0.16–0.84; p=0.018). Recurrence rates were significantly reduced (5.5% vs 13.8%; OR 0.36, 95% CI 0.17–0.75; p=0.006). MWA treatment remained an independent predictor of reduced recurrence on multivariable analysis (adjusted OR 0.35, 95% CI 0.16–0.76; p=0.007). Conclusion: Pit-picking combined with microwave ablation is a safe and effective minimally invasive treatment strategy for PSD, significantly improving postoperative recovery, reducing morbidity, and lowering recurrence rates. Further prospective randomized studies with longer follow-up are warranted.