Series of studies have described malnutrition as one of the main non-traditional risk factors associated with poor prognosis and treatment outcome in patients on hemodialysis (HD). The aims of this study were to evaluate the link between HD treatment quality and the nutritional status and to additionally investigate the association of malnutrition and overall survival. A total of 134 adult out-patients (56.4% male, mean age 60.8 ± 16.15 years) were enrolled in the study. Clinical and laboratory data were obtained from the medical records. Anthropometric measurements were performed prior to HD. Malnutrition-Inflammation Score (MIS) was used as a scoring system representing the severity of protein-energy wasting (PEW). Malnourished patients were significantly older when compared to non-malnourished patients. They had significantly longer dialysis vintage and lower residual diuresis, BMI, serum proteins, and albumins and lean tissue index (LTI). Malnourished patients survived significantly shorter than non-malnourished patients. Hypoproteinemic patients had significantly lower values of serum albumins and LTI and survived shorter than normoproteinemic patients. Only malnourishment and age were associated with higher overall mortality in all groups of patients. By focusing on MIS and serum protein status rather than dialysis-related factors and different treatment techniques, we could accomplish better nutrition status and improved overall outcomes. While anticipating new and more effective measures for preventing malnutrition, our results clearly demonstrate that striving for the highest possible nutrition status should be one of the key strategies in improving the outcomes in this specific group of patients.