Fourier Transform Infrared (FTIR) is an established analytical technique to elucidate new discriminatory biomarkers. Our previous study showed that Ficus deltoidea (Ficus: Moraceae) is capable of increasing insulin secretion and improving tissue regeneration by reducing oxidative stress in diabetic rats. However, the assessment of treatment response is limited by the paucity of biomarkers. We aimed to evaluate the potential use of FTIR for assessing the nephroprotective effects of Ficus deltoidea (Ficus: Moraceae) in diabetic rats. A rat model of diabetes was induced using a single intraperitoneal injection of streptozotocin (STZ) (60 mg/kg body weight). Methanolic extract of F. deltoidea was administered orally at a dose of 1000 mg/kg body weight for eight weeks. Fasting blood glucose, serum insulin and kidney function parameters were examined. The kidneys were subsequently subjected to FTIR and histological analyses. Enzyme-linked immunosorbent assays (ELISA) assessed the levels of oxidative stress, antioxidant, and apoptosis-related proteins in the kidney tissue. The results show, for the first time, that there is a good agreement between changes in kidney and FTIR peaks. The IR peaks (1545 cm−1 and 1511 cm-1) corresponding to amide II were restored by treatment with F. deltoidea. Multivariate analysis demonstrated that the diabetic rats treated with F. deltoidea had similar clustering pattern that of the normal animals. Biochemical and histological examination further confirmed the nephroprotective effect of F. deltoidea. Thus, demonstrating how FTIR spectroscopy could be used for the diagnosis of diabetes kidney disease.