The choice of dialysate buffer in hemodialysis is crucial, with acetate being widely used despite complications. Citrate has emerged as an alternative due to its favorable effects, yet concerns persist about its impact on calcium and magnesium levels. This study investigates the influence of citrate dialysate (CD) with and without additional magnesium supplementation on CKD-MBD biomarkers and assesses their ability to chelate divalent metals compared to acetate dialysates (AD). A prospective crossover study was conducted in a single center, involving patients on thrice-weekly online hemodiafiltration (HDF). Four dialysates were compared: two acetate-based and two citrate-based. Various biochemical parameters were monitored before and after each dialysis session. Seventy-two HDF sessions were performed in eighteen patients. CD showed stability in iPTH levels and reduced post-dialysis total calcium, with no significant increase in adverse events. Magnesium supplementation with CD prevented hypomagnesemia. However, no significant differences among dialysates were observed in the chelation of other divalent metals. Citrate dialysates, particularly with higher magnesium concentrations, offer promising benefits, including prevention of hypomagnesemia and stabilization of CKD-MBD parameters, suggesting citrate as a viable alternative to acetate. Further studies are warranted to elucidate long-term outcomes and optimize dialysate formulations.