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In this study, we aimed to use the Protection Motivation Theory (PMT) to explain farmers’ pro-environmental behavior, and we subsequently applied our conceptualization of the PTM to explain the effects of pro-environmental behavior as well as some alternatives to achieve a sustainable livelihood in the Borkhar Region, Isfahan Province, Iran. The population of this study comprised rural smallholder farmers who produced agricultural and horticultural crops under drought in 2017-2019. The study sample consisted of 293 smallholder farmers selected through stratified random sampling. A questionnaire was utilized for data collection, and data were analyzed using structural equation modeling. The findings suggest that self-efficacy, perceived vulnerability, and response efficacy have a positive relationship with farmers’ pro-environmental behavior. In addition, the perceived severity and response costs are negatively related to farmers’ pro-environmental behavior. The findings further show that alternative crops and alternative income sources are the main predictors of achieving a sustainable alternative livelihood. Moreover, saffron cultivation and rural handicrafts were found to be highly important indicators that enhance sustainable alternative livelihood under drought. Therefore, concentrating efforts and shifting the focus to these alternatives leads to increased farmers’ livelihood resilience in the long run.