This study assessed the impact of Tropical Cyclone Freddy on household sanitation facilities in a rural area of southern Malawi as part of two local non-government organisations’ routine programme monitoring and evaluation. Household surveys were conducted in 311 households at programme baseline in April 2022 before CLTS implementation activities started and combined with Community-led Total Sanitation (CLTS) open defecation verification data to estimate pre-Cyclone Freddy household sanitation access. A follow-up survey was repeated in the same households in June 2023, approximately three months after Cyclone Freddy landed in Chiradzulu District. These data were used to estimate changes in household sanitation facilities before and after Cyclone Freddy.