Introduction Timely diagnosis of iron deficiency is crucial for managing anemia in patients with non-dialysis-dependent chronic kidney disease (ND-CKD). However, iron status results are not always immediately available. We aimed to examine the performance of mean corpuscular volume (MCV) in diagnosing iron deficiency as a primary objective and of iron status in predicting the onset of iron deficiency as a secondary objective. Methods This retrospective cohort study included adult patients with ND-CKD from the BRIGHTEN (oBservational clinical Research In chronic kidney disease patients with renal anemia: renal proGnosis in patients with Hyporesponsive anemia To Erythropoiesis-stimulating agents, darbepoetiN alfa) trial (enrolled from June 2014 to September 2016) in Japan who were started on darbepoetin-alpha for renal anemia and patients who were not started on iron supplementation during weeks 0-24. Diagnostic performance analysis assessed the MCV at week 24 and changes in MCV from week 12 to 24 for diagnosing iron deficiency (ferritin < 100 ng/mL) at week 24, using receiver operating characteristic curves, area under the curve (AUC), sensitivity, and specificity. For the patients without iron deficiency at week 12, ferritin levels at week 12 were assessed by predictive performance analysis to predict new-onset iron deficiency at week 24. Results A total of 796 participants were included in the diagnostic performance analysis (mean age, 70.0 years; mean estimated glomerular filtration rate, 19.2 mL/min/1.73 m²), and 338 were included in the predictive performance analysis. Diagnostic performance analysis revealed an AUC for MCV of 0.55 (95% confidence interval (CI), 0.51-0.59); for MCV changes, it was 0.52 (95% CI, 0.48-0.57). Prognostic performance analysis revealed that ferritin at week 12 demonstrated an AUC of 0.77 (95% CI, 0.67-0.86), with a sensitivity of 83% and a specificity of 66% at a cutoff of 131.5 ng/mL. Conclusion Neither MCV nor the changes in MCV could reliably diagnose iron deficiency in patients with ND-CKD. Ferritin level < 130 ng/mL could predict new-onset iron deficiency within 12 weeks.