Plasma sodium shifts during hemodialysis treatments can be minimized by application of a sodium control algorithm. The present randomized cross-over trial was designed to apply this option on a large patient cohort and to observe the time course of plasma sodium over the treatment. In one study phase, patients received post-dilution online hemodiafiltration treatments with sodium control over the entire treatment. In the other study phase, patients received isolated ultrafiltration during the first 90 min followed by post-dilution online hemodiafiltration with sodium control for the remainder of the session, with the purpose to follow a possible initial equilibration process without the influence of a diffusive solute transfer. Each phase included six treatments and was delivered in randomized order. Eighty-one patients were enrolled, 77 patients could be analyzed as intention-to-treat population. The difference of the mean plasma sodium concentration between start and end of the treatment was −0.60 mmol/L (confidence interval −0.88 to −0.32) and −0.15 mmol/L (confidence interval −0.43 to 0.13), for sodium control and isolated ultrafiltration during the first 90 min followed by post-dilution online hemodiafiltration with sodium control, respectively. The functionality of the sodium control option could be confirmed and further reproduced in a bigger population of dialysis patients, providing the basis to investigate the clinical benefit of individually adjusting dialysate sodium in further clinical studies.