Competent authorities, healthcare payers and hospitals devote increasing resources for quality management systems but scientific analyses searching for an impact on clinical outcome remain scarce. Earlier data indicated a stepwise improvement in outcome after allogeneic hematopoietic stem cell transplantation with each phase of the accreditation process for the quality management system "JACIE". We therefore tested the hypothesis that working towards and achieving "JACIE" accreditation would accelerate improvement in outcome over calendar time. Overall mortality of the entire cohort of 107,904 patients with a transplant (41,623 allogeneic, 39%; 66,281 autologous, 61%) between 1999 and 2006 decreased over the 14 years observation period by a factor of 0.63 per 10 years (HR: 0.63; 0.58-0.69). This improvement was significantly faster with approx. 5.3% per year for the 49,459 patients transplanted in "JACIE " accredited centers, defined as programs having achieved accreditation the latest by November 2012, than the approx. 3.5% per year for the 58,445 patients in non accredited centers (HR: 0.83; 0.71-0.97). As a result, relapse free (HR 0.85; 0.75-0.95) and overall survival (HR 0.86; 0.76-0.98) were significantly higher at 72 months for those patients transplanted in the 162 "JACIE " accredited centers. No significant effects were observed after autologous transplants (HR 1.06; 0.99-1.13). Hence, working towards implementation of a quality management system triggers a dynamic process associated with a steeper reduction in mortality over the years and a significantly improved survival after allogeneic stem cell transplantation. Our data support the use of a quality management system for complex medical procedures.