Mitochondrial alterations are increasingly recognized as central to the pathogenesis of chronic kidney disease (CKD), contributing to impaired energy metabolism, oxidative stress, and maladaptive cellular responses. This review highlights recent advances in our understanding of mitochondrial remodeling in both diabetic and non-diabetic CKD (NDKD), including changes in bioenergetics, dynamics, redox balance, and biogenesis. We discuss state-of-the-art approaches to assess mitochondrial health, ranging from high-resolution respirometry and metabolomic profiling to transcriptomic analysis and advanced imaging techniques such as functional magnetic resonance imaging (MRI) and positron emission tomography (PET) radiotracers with metabolic readouts.