This study is embedded within the Water, Sanitation, and Hygiene for Everyone programme in Chiradzulu District, Malawi, where one programme area achieved Open Defecation Free (ODF) status in December 2022 following a Community-Led Total Sanitation (CLTS) intervention. In March 2023, Tropical Cyclone Freddy made landfall in Chiradzulu District, causing widespread damage to essential infrastructure. This study compares household sanitation access, classified according to the WHO/UNICEF Joint Monitoring Programme (JMP) sanitation ladder, before and after the cyclone in a rural area of southern Malawi. Household surveys were administered in the same 311 households at programme baseline in April 2022, prior to CLTS implementation, and at 10-month follow-up in June 2023, three months after Cyclone Freddy. ODF status verification data were also used to estimate pre-cyclone sanitation access. These data were used to estimate the proportion of household sanitation facilities that collapsed and became unusable due to the cyclone. The types of JMP sanitation facilities most prone to collapse and those most likely to be reconstructed three months after the cyclone are also reported. Of the 311 households surveyed, 5% had access to basic sanitation, 3% to limited sanitation, and 92% relied on unimproved sanitation prior to Cyclone Freddy. Following the cyclone, 68% of households reported that their sanitation facility, primarily unimproved, had collapsed. Three months later, 36% of surveyed households had no sanitation facility at all, while 50% relied on unimproved sanitation. Among the 211 households whose facility collapsed, 43% rebuilt an unimproved facility. These findings underscore the vulnerability of sanitation infrastructure to tropical cyclones, which can cause affected communities to resort to unsafe sanitation practices or rebuild facilities that remain vulnerable to future cyclones. Improving the resilience of household sanitation infrastructure to extreme weather is critical to protecting public health, particularly in the context of climate change.