Integrin-linked kinase (ILK) is a key scaffolding protein between extracellular matrix protein and the cytoskeleton and has been implicated previously in the pathogenesis of renal damage. However, its involvement in renal mitochondrial dysfunction remains to be elucidated. We studied the role of ILK and its downstream regulations in renal damage and mitochondria function both in vivo and vitro, using a folic acid (FA)-induced kidney disease model. Wild type (WT) and ILK conditional-knockdown (cKD-ILK) mice were injected with a single intraperitoneal dose of FA and studied after 15 days of chronic renal damage progression. Human Kidney tubular epithelial cells (HK2) were transfected with specific siRNAs targeting ILK, glycogen synthase kinase 3-β (GSK3β), or CCAAT/enhancer binding protein-β (C/EBPβ). The expressions and activities of renal ILK, GSK3β, C/EBPβ, mitochondrial oxidative phosphorylation enzymes, and mitochondrial membrane potential were assessed. Additionally, the expression of markers for fibrosis fibronectin (FN) and collagen 1 (COL1A1), for autophagy p62 and cytosolic light chain 3 (LC3B) isoforms II and I, and mitochondrial homeostasis marker carnitine palmitoyl-transferase 1A (CPT1A) were evaluated using immunoblotting, RT-qPCR, immunofluorescence, or colorimetric assays. FA upregulated ILK expression, leading to the decrease of GSK3β activity, increased tubular fibrosis, and produced mitochondrial dysfunction, both in vivo and vitro. These alterations were fully or partially reversed upon ILK depletion, mitigating FA-induced renal damage. The signaling axis composed by ILK, GSK3β, and C/EBPβ regulated CPT1A transcription as the limiting factor in the FA-based impaired mitochondrial activity. We highlight ILK as a potential therapeutical target for preserving mitochondrial function in kidney injury.