Abstract Introduction. Switching from polluting (e.g. wood, crop waste, coal) to clean (e.g. gas, electricity) cooking fuels can reduce household air pollution exposures and climate-forcing emissions. While studies have evaluated specific interventions and assessed fuel-switching in repeated cross-sectional surveys, the role of different multilevel factors in household fuel switching, outside of interventions and across diverse community settings, is not well understood. Methods. We examined longitudinal survey data from 24 172 households in 177 rural communities across nine countries within the Prospective Urban and Rural Epidemiology study. We assessed household-level primary cooking fuel switching during a median of 10 years of follow up (∼2005–2015). We used hierarchical logistic regression models to examine the relative importance of household, community, sub-national and national-level factors contributing to primary fuel switching. Results. One-half of study households (12 369) reported changing their primary cooking fuels between baseline and follow up surveys. Of these, 61% (7582) switched from polluting (wood, dung, agricultural waste, charcoal, coal, kerosene) to clean (gas, electricity) fuels, 26% (3109) switched between different polluting fuels, 10% (1164) switched from clean to polluting fuels and 3% (522) switched between different clean fuels. Among the 17 830 households using polluting cooking fuels at baseline, household-level factors (e.g. larger household size, higher wealth, higher education level) were most strongly associated with switching from polluting to clean fuels in India; in all other countries, community-level factors (e.g. larger population density in 2010, larger increase in population density between 2005 and 2015) were the strongest predictors of polluting-to-clean fuel switching. Conclusions. The importance of community and sub-national factors relative to household characteristics in determining polluting-to-clean fuel switching varied dramatically across the nine countries examined. This highlights the potential importance of national and other contextual factors in shaping large-scale clean cooking transitions among rural communities in low- and middle-income countries.