Market participation by smallholder indigenous crop farmers holds significant potential for the alleviation of food insecurity and poverty amongst rural households. Smallholder farmers generally play a vital role in the production and marketing of indigenous crops in South Africa. However, smallholder farmers continue to remain among the food-insecure populations. This is more worrisome for indigenous crop farming households whose produce is far more limited in the market yet may contribute towards improving their food security status and livelihoods. This study analysed the impact of market participation of indigenous crops on the household food security of smallholder farmers in the Limpopo and Mpumalanga provinces of South Africa. A sample size of 209 indigenous crop producers were selected from a population of 1520 smallholder farmers. The study adopted a multi-stage stratified random sampling technique. The data were collected using both qualitative and quantitative research and were analysed using descriptive analysis, Household Food Insecurity Access Scale (HFIAS), and the Poisson regression model with the endogenous treatment model. The household size, marital status, household members living with HIV, and access to extension services were found to be positive and significant in determining household food security, whereas the disability of a household member was significant but negative. While the number of smallholder farmers involved in the production of indigenous crops is still limited, enhanced marketing of indigenous crops may improve the food security status of smallholder farmers. There is still a need for the government to channel its interventions towards the indigenous crop production sector, and this may include the provision of trained extension officers to assist smallholder farmers. Policymakers need to develop policies that support the production and marketing of indigenous crops. More awareness and promotion of indigenous crops are needed to encourage more smallholder farmers to adopt this farming practice. Further study of smallholder indigenous farmers across nine provinces of South Africa should be conducted to obtain deeper and broader insights into the role of these farmers on household food security.