Abstract Background Schistosomiasis is a debilitating neglected tropical disease endemic in sub-Saharan Africa. The role of health facilities in the prevention, diagnosis, control, and elimination of schistosomiasis is poorly documented. In a setting targeted for schistosomiasis elimination in Zanzibar, we assessed the prevalence of Schistosoma haematobium among patients seeking care in a health facility and investigated schistosomiasis-related knowledge of staff, and health facilities’ capacities and needs for schistosomiasis diagnosis and management. Methods We conducted a health facility-based mixed-method study on Pemba Island from June to August 2023. Patients aged ≥ 4 years seeking care in four health facilities were screened for S. haematobium infection using urine filtration and reagent strips. Those patients aged ≥ 10 years were additionally interviewed about signs and symptoms. Staff from 23 health facilities responded to a questionnaire assessing knowledge and practices. Ten staff participated in a focus group discussion (FGD) about capacities and needs for schistosomiasis diagnosis and management. Results The prevalence of S. haematobium infection in patients attending the health facilities, as determined by the presence of eggs in urine, was 1.1% (8/712). Microhaematuria was detected in 13.3% (95/712) of the patients using reagent strips. Among patients responding to the questionnaire, pelvic pain, pain during sex, and painful urination were reported by 38.0% (237/623), 6.3% (39/623), and 3.2% (20/623), respectively. Among the health facility staff, 90.0% (44/49) and 87.8% (43/49) identified blood in urine and pelvic pain, respectively, as symptoms of urogenital schistosomiasis, 81.6% (40/49) and 93.9% (46/49) reported collecting a urine sample and pursuing a reagent strip test, respectively, for diagnosis, and 87.8% (43/49) administered praziquantel for treatment. The most reoccurring themes in the FGD were the need for more staff training about schistosomiasis, requests for diagnostic equipment, and the need to improve community response to schistosomiasis services in health facilities. Conclusions The prevalence of S. haematobium infection in patients seeking care in health facilities in Pemba is very low and similar to what has been reported from recent community-based cross-sectional surveys. The health facility staff had good schistosomiasis-related knowledge and practices. However, to integrate schistosomiasis patient management more durably into routine health facility activities, scalable screening pathways need to be identified and capacities need to be improved by regular staff training, and an unbroken supply of accurate point-of-care diagnostics and praziquantel for the treatment of cases. Graphical abstract