Purpose This study aims to analyze the quality of life in patients with an ileal pouch-anal anastomosis (IPAA) and to investigate the association between height and type of the anastomosis, the number of stage procedures and age, and the fecal continence outcomes. Methods This is a cross-sectional retrospective study in patients who had undergone IPAA between 1992 and 2016 (N = 133). We sent questionnaires to 102 eligible patients (64% response rate). We used the Wexner score to assess fecal incontinence: 0 = no incontinence to 20 = complete incontinence. We used RAND-36 to measure quality of life. Results Patients who underwent mucosectomy with hand-sewn anastomoses (n = 11, 17%) had significantly higher median Wexner scores than patients with stapled anastomoses (10 versus 3, P = 0.003). Lower anastomoses correlated significantly with increasing Wexner scores (r = - 0.468, P <0.001). Quality of life of incontinent patients was diminished. Patients who were older at the time of IPAA surgery had higher Wexner scores (P = 0.004), while the time between surgery and questionnaire did not influence their Wexner scores (P = 0.810). Considering the stage procedures, multiple linear regression showed that the two-stage procedure without diverting ileostomy was significantly associated with higher Wexner scores (B = 0.815, P = 0.02), adjusted for sex (P = 0.008) and anastomosis type (P = 0.002). The three-stage procedure showed equally low complications and anastomotic leakage rates. Conclusion Mucosectomy with more distal, hand-sewn anastomosis and increasing age at IPAA surgery was associated with poorer fecal continence outcomes. The three-stage procedure appears to give the best fecal continence results without increasing complications. Furthermore, incontinence reduced patient's quality of life.