The prevalence of organic farming and other sustainability standards is increasing around the globe. While effects of organic farming on productivity, income, and poverty alleviation have been analyzed in numerous empirical studies, its effects on food security are barely understood. Using data from smallholder cotton farmers in Benin, we aim to empirically investigate how adopting organic farming affects their food security. According to our results, organic farming is conditionally associated with a notably lower experienced food security and a slightly lower dietary diversity and consumption of vitamin A-rich foods. Evaluating pathways, we find that the negative conditional association between organic farming and food security is a result of a lower household income of organic farms due to lower income from cotton farming given a smaller land area cultivated with cotton, while a larger land area cultivated with food crops cannot fully compensate for the reduced income from cotton farming. This alarming result illustrates the need for evaluating and eventually improving programs for organic farming in developing countries to ensure that good intentions for more sustainable production practices do not jeopardize the livelihoods of vulnerable smallholder farmers.