Background T cells play a crucial role in immune responses and are involved in chronic diseases such as Type 2 Diabetes Mellitus (T2DM) and its complications, including Diabetic Nephropathy (DN). Among these, regulatory T cells (Treg) act as key regulators, while T helper 9 (Th9) cells, which produce IL-9, are essential in maintaining immune balance. Methods The study included 145 participants divided into four groups: T2DM with nephropathy (35), T2DM without nephropathy (35), non-diabetic chronic kidney disease (ND-CKD) (35), and healthy controls (35). Various assessments were conducted, including anthropometric measurements, biochemical analyses, gene expression analysis was performed using RT-qPCR to profile mRNA and miRNA expression levels, flow cytometry (immune cell populations), and cytokine analysis by ELISA. Statistical analyses were carried out using SPSS, jamovi, Orange Data Mining, and Excel, ensuring robust evaluation and interpretation of the data. Results Th9 cells correlated with IL-9 (r = 0.72, p < 0.01), and Treg cells with IL-10 (r = 0.68, p < 0.01). The Th9/Treg ratio significantly increased across groups (chi(2) = 14.8, p < 0.001), with notable differences between HC and T2DM (p = 0.009) and HC and DN (p < 0.001). IL-9 (AUC = 0.880) and Th9/Treg ratio (AUC = 0.762) showed potential as DN diagnostic markers. PTEN levels were reduced in DN and ND-CKD (p < 0.001, p = 0.017), while MMP2, hsa-miR-21-5p, and hsa-miR-181b-5p were elevated in disease groups (all p < 0.001), correlating with renal markers. COL4A4 was higher in DN vs. HC (p = 0.004), with PTEN downregulation linked to immune imbalance and fibrosis. Conclusion Our study unveils immune cell and cytokine intricacies in DN. The high Th9/Treg ratio in T2DM and DN suggests immune tolerance loss, potentially influencing DN development. IL-9 and IL-10 display diagnostic potential. The Th9/Treg ratio and IL-9 serves as a discriminative diagnostic marker, particularly in DN. These insights offer avenues for early DN diagnosis and management.