Aim: Pilonidal sinus disease (PSD) primarily affects young adults; rapid recovery is essential and yet lacks a standardized treatment approach. While excisional techniques delay recovery, minimally invasive options like laser ablation and phenol application are gaining interest, yet comparative long-term evidence is scarce. This study compared short- and long-term outcomes of laser versus phenol treatment in PSD. Method: In this multicentre retrospective cohort study (Nov. 2017–Sep. 2024), patients treated with laser or phenol were included. 1:3 propensity score matching using the nearest neighbour algorithm was performed based on age, gender, prior surgical history and year of operation. Categorical variables were analysed using chi-squared or Fisher's exact tests, whereas continuous variables were compared using Student's t-test or Mann–Whitney U test depending on distribution normality. Results: Out of 897 eligible patients, 644 were included (median age: 26 years, body mass index [BMI]: 26.2 kg/m2, male-to-female ratio: 4:1). The number of sinuses/pits was 2–3 in both groups. Operating time was significantly longer in the laser group. Complications occurred in 6.8% of laser patients, whereas none were reported in the phenol group. Pain scores were higher in the laser group (2 [1–3] vs. 1 [0–2]). Median follow-up was 45 months (laser) and 40 months (phenol). Return to daily activities was delayed in the laser group, whereas complete healing was slower in the phenol group. Readmission, recurrence and recovery rates were comparable (85%–86%). Conclusion: Both treatments demonstrated low complication and recurrence rates with high recovery rates. Laser favoured faster healing and fewer sessions, whereas phenol allowed for shorter procedures and earlier return to daily life.