The colliding epidemic of infectious and non-communicable diseases in South Africa could potentially increase the prevalence of kidney disease in the country. This study determines the prevalence of kidney damage and known risk factors in a rural community of the Eastern Cape province, South Africa. This observational cross-sectional study was conducted in the outpatient department of the Mbekweni Community Health Centre in the Eastern Cape between May and July 2022. Relevant data on demography, medical history, anthropometry and blood pressure were obtained. The glomerular filtration rate was estimated using the Chronic Kidney Disease Epidemiology Collaboration Creatinine (CKD-EPICreatinine) equation and the re-expressed four-variable Modification of Diet in Renal Disease (MDRD) equation, without any adjustment for black ethnicity. Prevalence of kidney damage was defined as the proportion of individuals with low eGFR (<60mL/min per 1.73m2). The presence of proteins in the spot urine samples was determined with the use of test strips. We used the logistic regression model analysis to identify the independent risk factors for significant kidney damage. The mean (±standard deviation) age of the 389 participants was 52.3 (± 17.5) years, with 69.9% female. The prevalence of significant kidney damage was 17.2% (n = 67), as estimated by the CKD-EPICreatinine, with a slight difference by the MDRD equation (n = 69; 17.7%), while the prevalence of proteinuria was 7.2%. Older age was identified as a significant risk factor for CKD, with an odds ratio (OR) = 1.08 (95% confidence interval [CI]: 1.06-1.1, p < 0.001). Hypertension was strongly associated with proteinuria (OR = 4.17, 95% CI 1.67-10.4, p<0.001). This study found a high prevalence of kidney damage (17.2%) and proteinuria (7.97%) in this rural community, largely attributed to advanced age and hypertension, respectively. Early detection of proteinuria and decreased renal function at community health centres should trigger a referral to a higher level of care for further management of patients.