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A cross-sectional study was applied to investigate the influence of food systems and food environments on food choices and nutrition transition of households in Limpopo province, South Africa. A sample of 429 households were systematically selected using a paper selection draw from three districts. Food systems, food environments, food choices, and nutritional measurements of the households and informants were assessed, using a validated questionnaire. Most of the household informants responsible for food procurement were females (80.4%). There was a significant association (p< 0.001) between proximity to food stores and dietary diversity of the households. Staple foods were available in almost all surveyed households (95.6%). More than half of the households (59.8%) had home gardens in their yards. Almost half of the households (48.4%) had a low Dietary Diversity Score. The study revealed that 46.0% of households were food secure. Over a third (36.2%) of households’ informants were obese and 32.5% were diabetic. The mean total blood cholesterol was 3.69±0.74 mmol/L. A high percentage of both females (89.6%) and males (91.5%) had normal haemoglobin levels. Most of the informants had normal systolic blood pressure levels (63%), with just over half who had high diastolic levels (57%). The 25 coping strategies were applied during food shortages periods. Even though the food environments provided both obesogenic and protective foods, the consumption of unhealthy foods was high.