Abstract Purpose There is no consensus on the standard approach for trans-sphincteric perianal fistulas (TPAF) in the elderly population. The most commonly used sphincter-saving procedures are ligation of the inter-sphincteric fistula tract (LIFT) and mucosal advancement flap (MAF). We aimed to evaluate the incidence and risk factors for recurrence and incontinence in elderly patients with TPAF using both approaches. Methods This retrospective study included 257 patients who underwent LIFT (136 patients) or MAF (121 patients) for de novo and cryptoglandular TPAF between July 2018 and July 2021. Recurrent fistulas were clinically and radiologically detected using MRI. Postoperative incontinence was evaluated using the Wexner score and anorectal manometry. Logistic regression analysis was used to detect the risks of recurrence and incontinence. Results The median ages of the patients were 68 (64, 74) and 68 (65, 74) years in the LIFT and MAF groups, respectively. Higher recurrence rates were observed after LIFT (17 (12.5%)) than after MAF (13 (10.7%)), but the difference was not statistically significant (P = 0.662). Postoperative incontinence was observed in 18 patients (13.2%) and seven patients (5.8%) in the LIFT and MAF groups, respectively (P = 0.044). The predictors for fistula recurrence were smoking (OR, 75.52; 95% CI, 1.02 to 5611.35; P = 0.049), length of tract (OR, 17.3; 95% CI, 1.49 to 201.13; P = 0.023), and CD classification (OR, 7.08; 95% CI, 1.51 to 33.14; P = 0.013). A low Charlson comorbidity index score (≤ 5) (OR, 0.68; 95% CI, 0.47 to 0.99; P = 0.046) and high postoperative mean squeeze anal pressure (OR, 0.97; 95% CI, 0.95 to 0.99; P = 0.001) were significant factors associated with reduced risk of incontinence. In particular, LIFT was associated with a significantly higher risk of incontinence than MAF (OR, 2.089; 95% CI, 1.006 to 4.33; P = 0.04). Conclusions The healing rates of MAF and LIFT procedures did not differ significantly; however, continence was significantly better after MAF. MAF should be added to the guidelines as a good option for the treatment of TPAF in elderly patients.