Background Hyperglycaemia influences the development of glomerular endothelial cell damage and nowhere is this more evident than in the progression of diabetic kidney disease (DKD). While the Set7 lysine methyltransferase is a known hyperglycaemic sensor, its role in endothelial cell function in the context of DKD remains poorly understood. Methods Single-cell transcriptomics was used to investigate Set7 regulation in a mouse model of DKD, followed by validation of findings using pharmacological and shRNA inhibition of Set7. Results Set7 knockout (Set7KO) improved glomerular structure and albuminuria in a mouse model of diabetes. Analysis of single cell RNA-seq (scRNA-seq) data showed dynamic transcriptional changes in diabetic renal cells. Set7KO controls phenotype switching of GEN cell populations through transcriptional regulation of IGFBP5 (Insulin growth factor binding protein 5). Chromatin immunoprecipitation assays confirmed the expression of the IGFBP5 gene was associated with mono- and di-methylation of histone H3 lysine 4 (H3K4me1/2). The generalisability was investigated in human renal and circulating hyperglycaemic cells exposed to TGFβ1. We show that the highly selective Set7 inhibitor, PFI-2, attenuated indices associated with renal cell damage and mesenchymal transition; specifically (i) reactive oxygen species production, (ii) IGFBP5 gene regulation, and (iii) expression of mesenchymal markers. Furthermore, renal benefit observed in Set7KO diabetic mice closely correspond in human GEN cells with PFI-2 inhibition or Set7 shRNA silencing. Conclusions Set7 regulates the phenotypic endothelial-mesenchymal transition (EDMT) switch and suggest that targeting the lysine methyltransferase could protect glomerular cell injury in DKD.