Livestock production systems are essential for sustaining household food security, especially in the drylands of Africa. This study assesses the impact of South Africa’s targeted Large Stock Unit (LSU) social protection program on the acute food insecurity effects of the COVID-19 pandemic among selected smallholder livestock farmers. An embedded research approach was utilized in four local municipalities purposively selected in the Northern Cape Province, where 217 households were selected using a stratified proportionate random method. A structured questionnaire was employed, while secondary data on beneficiary farmers were collected from implementing agencies. A full information maximum likelihood (FIML) Endogenous Switching Regression (ESR) model was adopted to capture variations due to self-selection bias among respondents. ESR model results show that the decision maker’s age, the household head’s education level, the land holdings’ size, average relative livestock losses, the orientation of production, and the level of external support impact food security. The study concludes that based on average treatment effects analysis, beneficiaries of the LSU program are better off in the household food security relative to their non-beneficiary counterparts. These findings validate the need for enhancing support initiatives during COVID-19 shocks for households to attain food security using their main livelihood sources as the gateway. Increasing the diversity of livelihood strategies in these vulnerable communities needs to be scaled up to protect households from acute food insecurity. Targeted support programs, including direct financing and binding networks, may also be supported through youth-sensitive training programs to enhance mitigations and resilience against COVID-19 acute food insecurity. A policy can tap into existing local structures and province-wide institutional platforms for the long-term sustainability of the LSU support initiatives and mitigation of COVID-19 food security vulnerabilities.