Smallholder farmers who rely on home garden agroforestry are experiencing significant impacts from climate change. To mitigate these effects, it is crucial for farmers to have access to various adaptation strategies. This study collected data from 384 randomly selected respondents in 18 kebeles over three districts, using descriptive statistics and a multivariate probit model to evaluate the factors influencing smallholder farmers’ decisions on their adaptation strategies against climate change. In Ethiopia’s Gedeo zone, this study found that smallholder farmers employ a range of adaptation methods, including expanding their agroforestry system, implementing modern agriculture techniques, conserving soil and water, diversifying their livelihoods, and employing various coping mechanisms. By analyzing data using the multivariate probit model, this study found several factors that had a significant impact on smallholder farmers’ choice of adaptation options. These factors include social network, age, education level, farming experience, household size, cultivated land size, annual income, and livestock holding. In addition, factors such as perception of climate change, previous experience of crop failure, recurrent drought, and access to information about climate change, occurrence of frost, agricultural extension contacts, access to farmer-to-farmer extension services, and perception of land infertility also influence their decision-making process. Our findings highlight the importance of improving institutional services in rural areas, promoting education on climate change, and strengthening social networks to enhance the ability of smallholder farmers to cope with the effects of climate change.