Access to functional and clean toilets which maintain privacy and dignity and support girls’ Menstrual hygiene management (MHM) plays a crucial role to getting girls back to school post-disaster. This could also help in managing feelings of shame and disgust experienced when using toilets in schools in post disaster settings. In this paper, we report on our assessment of water, sanitation and hygiene (WASH) facilities in schools three-years post the 2018 multi-hazard event in Indonesia. We used a mixed-methods approach using visual observations, interviews with school principals, surveys with schoolgirls and focus group discussions with schoolgirls and teachers to understand the lived experiences of students using toilets at school. Our results highlight that across schools descriptive and injunctive social norms were supportive of littering, inadequate toilet facilities for girls to manage their menstruation and bullying and antisocial behaviour by opening toilet doors while the facilities were occupied. Based on these results, we developed two types of interventions, physical and behavioural, piloted in three schools to increase WASH and MHM awareness and the safety of sanitation facilities. Our interventions showed that approaches for WASH interventions in schools can only be designed if we understand the local barriers to carrying out interventions that integrate maintenance plans. We provide recommendations to support practitioners in mitigating risk and improving circumstances for girls in schools in Indonesia, which have the potential to address SDG 4 on inclusive and equitable education and SDG 5 on gender equality and girls’ empowerment.