Background: Lower extremity amputation (LEA) in individuals with diabetes is a serious health issue with a considerable physical and social burden. The aim of this study was to assess the prevalence and risk factors associated with LEA in diabetic foot ulcer (DFU) patients. Materials and Methods: This was a cross-sectional health facility-based study that recruited 315 diabetes individuals with foot ulcers from the diabetes center in Khartoum, Sudan. Direct interviewing of subjects was used to obtain data, using a standardized validated questionnaire. Chi-square and logistic regression analysis were used in data analysis. Results: 69.5% of the diabetic participants were aged 50 years old or more, and 71.1% were males. Most of the subjects (48.2%) were diabetics for a duration of >10 years, while more than one third (37.5%) of them were diabetic for 5–10 years. The majority (89.5%) had type 2 DM, while only 10.5% were type 1 DM. Two hundred forty-five patients had a left lower foot ulcer; 55.1% of the patients' ulcers were present in the toes, while 21.6% were in the foot sole. The overall prevalence of lower limb amputation was 17.1%. Individuals with diabetes patients with LEA had a higher incidence of hypertension ( P = 0.000), retinopathy ( P = 0.000), nephropathy ( P = 0.002), ulcer size >2.5 cm ( P = 0.000), and neuropathy ( P = 0.000) through Chi-square analysis. Furthermore, logistic regression analysis showed that amputation was significantly associated with retinopathy ( P = 0.000), size of ulcer ( P = 0.000), and neuropathy ( P = 0.016). Conclusion: The overall prevalence of LEA was 17.1%. The primary risks factors associated with amputation were presence of neuropathy and ulcer size >2.5 cm. Presence of retinopathy predispose diabetic individuals to amputation. Amputation is associated with disability and psychological problems; therefore, there is an urgent need for more improvement in preventative measures and primary health care system in low resource setting country like Sudan in order to decrease diabetes complications, especially patient's education about diabetes management by primary care physicians.