Segmenting population into subgroups with higher intergroup, but lower intragroup, heterogeneity can be useful in enhancing the effectiveness of many socio-economic policy interventions; yet it has received little attention in promoting clean cooking. Here, we use PERMANOVA, a distance-based multivariate analysis, to identify the factor that captures the highest intergroup heterogeneity in the choice of cooking fuels. Applying this approach to the post-earthquake data on 747,137 households from Nepal, we find that ethnicity explains 39.12% of variation in fuel choice, followed by income (26.30%), education (12.62%), and location (4.05%). This finding indicates that ethnicity, rather than income or other factors, as a basis of policy interventions may be more effective in promoting clean cooking. We also find that, among the ethnic groups in Nepal, the most marginalized Chepang/Thami community exhibits the lowest intragroup diversity (Shannon index = 0.101) while Newars the highest (0.667). This information on intra-ethnic diversity in fuel choice can have important policy implications for reducing ethnic gap in clean cooking.