OBJECTIVES: To examine the association between facility-level adherence to phosphorus management guidelines and mortality among patients with haemodialysis, and to explore the facility-related factors associated with facility-level guideline adherence. DESIGN: Prospective cohort study. SETTING: The Dialysis Outcomes and Practice Pattern Study, which included 57 representative dialysis facilities in Japan between 2012 and 2015. PARTICIPANTS: A total of 2054 adult patients who received maintenance haemodialysis were included. We defined exposure according to the following four categories, depending on whether facility-level target ranges of serum phosphorus concentration adhered to the Japanese clinical practice guidelines: adherence group (lower limit ≥3.5 mg/dL and upper limit ≤6.0 mg/dL), low-target group (lower limit <3.5 and upper limit ≤6.0), wide-target group (lower limit <3.5 and upper limit >6.0) and high-target group (lower limit ≥3.5 and upper limit >6.0). PRIMARY OUTCOME MEASURE: The primary outcome was the patient all-cause mortality rate. RESULTS: The mortality rate among the patients was 7.3 per 100 person-years; 27 facilities (47%) set targets according to the guidelines. HRs for mortality with reference to the adherence group were 1.04 (95% CI 0.76 to 1.43) in the low-target group, 1.11 (95% CI 0.68 to 1.81) in the wide-target group and 1.95 (95% CI 1.12 to 3.38) in the high-target group. Involvement of dieticians in dialysis treatment was associated with facility-level guideline adherence (OR 4.51; 95% CI 1.15 to 17.7). CONCLUSIONS: A higher facility-level target range for phosphorus was associated with increased patient mortality. Among facilities that set the target according to the guidelines, dieticians tended to be involved in dialysis care. These findings suggest the importance of reviewing facilities' treatment policies in relation to updated guidelines and the need to work with relevant professionals.