Studies on the effect of dietary protein intake (DPI) on chronic kidney disease (CKD) progression, along with the potential hazard of protein-energy wasting (PEW), are scarce. We evaluated the association between DPI and kidney function both cross-sectionally and longitudinally, particularly emphasizing the role of PEW, in a large-scale, observational, multicenter, prospective study. We enrolled 1572 patients with non-dialysis CKD between 2011 and 2016. CKD progression was defined by a >50% estimated glomerular filtration rate (eGFR) decrease, serum creatinine doubling, or dialysis initiation. A Cox proportional hazard regression analysis was conducted. During the mean follow-up period of 41.6 months, CKD progression was observed in 296 patients. Cross-sectionally, increased DPI was significantly associated with increased eGFR. Similarly, increased DPI tertile was significantly associated with increased renal survival in a Kaplan⁻Meier curve analysis. In the multivariate Cox proportional hazard regression analysis, the statistical significance of the DPI tertile group in CKD progression was lost when PEW-related variables were added as covariates. In penalized spline curve analysis, the adjusted odds ratio of PEW significantly increased as DPI decreased. DPI, per se was not a major determinant of CKD progression. An intimate association between reduced DPI and PEW may be a more important predictor of CKD progression than DPI.