Abstract Background Microvascular complications of diabetes including retinopathy, nephropathy, and neuropathy are those long-term complications that affect small blood vessels. Diabetic nephropathy (DN) is characterized by persistent microalbuminuria. A meta-analysis of case–control studies aims to examine the relationship between MnSOD (rs4880) and GPx1 (rs1050450) and the risk of DN. Methods Various databases such as Web of Science, PubMed, Springer Link, Cochrane Library, Science Direct, Embase, and Google Scholar were utilized to extract relevant studies. The statistical software MedCalc version 22.009 was acquired to accomplish the meta-analysis of the included studies. Results A significant association was found between two SNPs (rs4880 and rs1050450) and DN in the homozygous recessive model [95% confidence interval (CI) 0.97–2.41, odds ratio (OR) TT vs CC = 1.53, P = 0.06] and heterozygous model [95% CI 0.92–1.97, OR CT vs CC = 1.35, P = 0.12], while there was no association with the other genetic models. A significant association between rs4880 and DN was perceived in the Asian population [95% CI 1.24–2.03, OR = 1.6, P < 0.001], meanwhile the studies among Caucasian group showed insignificant association [95% CI 0.87–1.32, OR = 1.07, P = 0.5]. On the other hand, the association between rs1050450 and DN was significant [95% CI 3.80–13.01, OR = 7.04, P < 0.001] and insignificant [95% CI 0.96–2.28, OR = 1.48, P = 0.07] among Asian and Caucasian population, respectively. Conclusion To date, this meta-analysis could be the first to contribute a panoramic exploration of the MnSOD and GPx1 polymorphic association with DN. The results of the study contemplate the data presently accessible from the literature and can be employed as an influential lead for future research.