Natural gas is widely used for household cooking, with methane (CH₄), its main component, being a potent short-lived greenhouse gas (GHG). While often seen as a cleaner alternative, natural gas combustion and leaks contribute to GHG emissions and indoor air pollution. Yet, fugitive methane emissions from residential appliances, especially cookstoves, are poorly quantified in low- and middle-income countries. In this study, we measured CH₄, carbon dioxide (CO₂), carbon monoxide (CO), and nitrogen oxides (NOx) emissions from cookstoves in 35 homes in Santiago, Chile, and 23 in Bogotá, Colombia, two countries experiencing rapid growth in natural gas use. We assessed continuous methane leaks, ignition-related emissions, and combustion emissions, using a mass balance approach that accounts for air exchange rates and gas concentrations. Our real-world measurements provide rare data on household cookstove emissions and inform emission factors used in GHG inventories. We found that methane emissions from residential stoves in Bogotá and Santiago are over six times higher than the Tier 1 IPCC emission factors currently used in national inventories. Notably, continuous leaks and ignition-related emissions, which are excluded from official estimates, contribute significantly to total methane emissions. These findings suggest that national inventories in Chile and Colombia underestimate methane emissions from household gas use, highlighting the need for more real-world measurements and research across Latin America. Our results have important implications for improving the accuracy of GHG inventories, understanding the role of household energy use in climate change, and guiding effective mitigation strategies.