Conditioning protocols for patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT) are being developed continuously to improve their anti-leukemic efficacy and reduce their toxicity. In this study, we compared the conditioning protocol of fludarabine with melphalan (FluMel) with conditioning protocols based on this same backbone but with an additional alkylating agent i.e. either fludarabine/BCNU (also known as carmustine)/melphalan (FBM), or fludarabine/thiotepa/melphalan (FTM) from the ‘intermediate’ transplantation conditioning intensity (TCI) score. We included 1551 adult patients (1139 patients with FluMel and 412 patients with FBM/FTM) with acute myeloid leukemia (AML) with intermediate/poor cytogenetic risk in first complete remission (CR) from the registry of the EBMT Acute Leukemia Working Party. In the FBM/FTM group, patients were older (62.4 years vs. 59.9 years, p < 0.001), had a worse Karnofsky performance score (KPS < 90, 31.2% vs. 22.7%, p < 0.001) and received more often grafts from unrelated donors (77.9% vs. 66.6%, p < 0.001), associated with worse overall survival (OS). Patients conditioned with FluMel more often received an in vivo T-cell depletion (85 vs 90%, p < 0.01) based on alemtuzumab (21% vs. 69%) whereas patients conditioned with FBM/FTM received more frequently anti-thymocyte globuline (78% vs. 7%). Patients in the FBM/FTM group showed a better OS (2y OS: 69.9% vs. 57.9%, hazard ratio (HR) 0.62, p < 0.001), leukemia-free survival (LFS) (2y LFS: 61% vs. 53.5%, HR 0.74, p = 0.004), and less non-relapse mortality (NRM) (2y NRM: 14.6% vs. 22%, HR: 0.54, p < 0.001) compared to patients treated with FluMel. No significant differences were observed in relapse incidence (RI) (2y RI: 24.3% vs. 24.5%, HR: 0.95, p = 0.73). Multivariate analysis confirmed improved outcomes (OS, LFS and NRM) in patients treated with FBM/FTM and no significant difference in RI. In conclusion, the addition of a second alkylating agent (BCNU/carmustine or thiotepa) to FluMel as FBM/FTM conditioning, improves OS after allo-HCT in AML patients in CR with intermediate/poor risk cytogenetics.