Chronic kidney disease (CKD) is associated to an increased risk of death, CKD progression and acute kidney injury (AKI) even from early stages, when glomerular filtration rate (GFR) is preserved. The link between early CKD and these risks is unclear, since there is no accumulation of uremic toxins. However, pathological albuminuria and kidney inflammation are frequent features of early CKD and the production of kidney protective factors may be decreased. Indeed, Klotho expression is already decreased in CKD category G1 (normal GFR). Klotho has anti-aging and nephroprotective properties and decreased Klotho levels may contribute to increase the risk of death, CKD progression and AKI. In this review, we discuss the downregulation by mediators of inflammation of molecules with systemic and/or renal local protective functions, exemplified by Klotho and peroxisome proliferator-activated receptor gamma coactivador-1α (PGC-1α), a transcription factor that promotes mitochondrial biogenesis. Cytokines such as TWEAK, TNFα or TGFβ1 produced locally during kidney injury or released from inflammatory sites at other organs may decrease kidney expression of Klotho and PGC-1α or lead to suboptimal recruitment of these nephroprotective proteins. Transcription factors (e.g. Smad3, NF-B) and epigenetic mechanisms (e.g. histone acetylation or methylation) contribute to downregulate the expression of Klotho and/or PGC-1α, while histone crotonylation promotes PGC-1α expression. NFBiz facilitates the repressive effect of NF-B on Klotho expression. A detailed understanding of these mediators may contribute to develop novel therapeutic approaches to prevent CKD progression and its negative impact on mortality and AKI.