Rates of anemia among agricultural workers, who are also at risk for kidney injury and chronic kidney disease of unknown cause (CKDu), are unknown. We evaluated body composition through the sum of three skinfolds among 203 male sugarcane cutters and assessed the relationship of variables related to nutrition, anemia (hemoglobin < 13 g/dL), and elevated hemoglobin A1c (HbA1c ≥ 5.7%) with estimated glomerular filtration rate (eGFR) using linear regression. Eleven percent of workers were at the level of essential body fat (2–5%). Anemia was present among 13% of workers, 70% of which were normochromic normocytic, a type of anemia suggesting potential underlying chronic disease. Anemia was more common among those with lower BMI and fat free mass. The prevalence of elevated HbA1c was 21%. A moderate negative correlation was found between hemoglobin and HbA1c (Pearson’s r = −0.32, p < 0.01) which suggests that HbA1c values should be interpreted with caution in populations that have high rates of anemia. Twelve percent of workers had reduced kidney function with an eGFR < 90 mL/min/1.73 m2. On average, the eGFR was 18 mL/min per 1.73 m2 lower [(95% CI:−24, −12), p < 0.01)] for those with anemia than those without, and 8 mL/min per 1.73 m2 lower among those with elevated HbA1c [(95% CI: −13, −2), p < 0.01]. Results will inform future studies examining the role of anemia in the evaluation of CKDu and interventions to improve nutrition for workers in low-resource settings.