Background: Along with a nutritional transition in Sub-Saharan Africa, the prevalence of non-communicable diseases is increasing rapidly. We assess the association between food intake and cardiometabolic risk factors in a rural population in Uganda. Methods: The present study was based on data from a household-based case-control study of diabetic and non-diabetic households in Southwestern Uganda, 2012–2013. We analysed food intake in 359 individuals age ≥ 13 years from 87 households, using a household food frequency questionnaire, and measures of glycated haemoglobin (HbA1c), height and weight. We used multinomial logistic regression to model abnormal HbA1c (≥5.7%) and weight status (underweight, normal weight and overweight) as an outcome of total food intake and by nine food groups. Results were reported as odds ratios (OR) with 95% confidence intervals (CI). Models were adjusted for three nested sets of covariates. Results: The diet primarily consisted of staple food (cassava and plantain). High-Glycaemic Index staple food was the most consumed food group (median = 14 servings/week, p25-p75: 11–17). Milk, meat, fish and vegetables were the least consumed food groups (medians: 0–3 servings/week). Median intake of sugary food was 6 servings/week (p25-p75: 2–9). The OR of having abnormal HbA1c or being overweight increased with every weekly serving of food (1.02, 95% CI: 1.00–1.04 and 1.01 95% CI: 1.00–1.03, respectively). Of specific food groups, each weekly serving of meat increased the OR of being overweight with 33% (95% CI: 1.08–1.64), and fruit intake decreased the OR of abnormal HbA1c (0.94, 95% CI: 0.88–1.00), though this latter association was attenuated after adjustment for weight status, aerobic capacity, and socioeconomic status. Conclusion: Diet was monotonous, mainly consisting of cassava and plantain, and increasing food intake was associated with abnormal HbA1c and overweight. To prevent non-communicable diseases a diet with higher intake of fish and vegetables, and less sugary food is recommended.