High crop productivity has the potential to improve the food and nutrition security status of not only smallholder farmers but also households in general. However, smallholder farmers operate in a dynamic environment whereby their crop production is affected by various factors that hinder it from lessening food insecurity and malnutrition in rural areas. The study investigated the determinants of crop productivity and its effect on household food and nutrition security status in South Africa. Methods: This study employed a quantitative research method. A total of 1520 households were selected using the multi-stage stratified random sampling technique. Out of the total sample size of 1520, 386 were crop producers, 176 producers were from Mpumalanga province, and 210 producers were from the Limpopo province. Results and discussion: Most of the smallholder farmers do not have access to the irrigation system, mechanization, and agricultural inputs. The Household Food Insecurity Access Scale showed that most smallholder farmers were food insecure, with 78% of the farmers in each province found to be food insecure. The results from Household Dietary Diversity Score (HDDS) showed that in the overall sampled population, 50% of smallholder farmers had highly diverse diets. Only 50% of the smallholder farmers had high dietary diversity in each province. Irrigation systems and involvement in crop production had a positive influence on the crop productivity of smallholder farmers. The results from the Conditional Mixed Process (CMP) model showed that ownership of livestock, harvest, and disability in the family negatively impacted smallholder farmers' food security status while household size had a positive effect on the food security of smallholder farmers. The results also showed that social grants, agricultural assistance, and harvest had a negative impact on the nutrition status of smallholder farmers. While household size had a positive impact on the nutrition status of smallholder farmers. Conclusion and recommendations: Factors such as irrigation systems and involvement in crop production influenced crop productivity. Household size influenced the nutritional status of smallholder farmers while harvest size affected the food security status. There is a need to encourage more households to get involved in farming. Government and non-governmental organizations need to support smallholder farmers with agricultural productive resources like irrigation systems to improve their crop productivity.