Myelodysplastic syndromes (MDS) mainly affect the elderly population, which implies that the majority of patients cannot tolerate intensive therapeutic approaches, including allogeneic hematopoietic stem-cell transplantation (allo-HSCT). The underlying impaired stem-cell function leads to peripheral cytopenia, including a propensity to progress to acute myeloid leukemia. Allo-HSCT is considered the only potentially curable therapy. Reduced-intensity conditioning regimens have shown to improve early tolerability of the procedure, but late effects like graft-versus-host disease and relapse remain major challenges in the care of these patients. Therefore, special attention should be paid to posttransplantation care in terms of graft-versus-host disease management, measurable residual disease monitoring, and prevention of relapse. In fact, recent advances in the field have shown that minimal residual disease measurement and preemptive therapies may be a promising approach to prevent or at least delay relapse. This review briefly discusses indication and selection of patients for allo-HSCT in MDS, pretransplantation evaluation and choice of conditioning regimens, and prophylactic and preemptive approaches to prevent relapse after allo-HSCT.