We prospectively studied CloFluBu-conditioning in allogeneic Hematopoietic Cell Therapy (HCT) for lymphoid- and myeloid malignancies, and hypothesized that CloFluBu provides a less toxic alternative to conventional conditioning regimens, with adequate anti-leukemic activity. All patients receiving their first HCT, from 2011-2019, were included and received CloFluBu. Primary endpoint was Event Free Survival (EFS). Secondary endpoints were Overall Survival (OS), Graft-versus-Host-Disease (GvHD)-Relapse-Free Survival (GRFS), Treatment Related Mortality (TRM), Cumulative Incidence of Relapse (CIR), acute and chronic GvHD, and veno-occlusive disease (VOD). Cox Proportional Hazard- and Fine and Gray competing-risk models were used for data analysis. 155 Children were included; 60 acute lymphoid leukemia (ALL), 69 acute myeloid leukemia (AML), and 26 other malignancies (mostly MDS-EB). Median age was 9.7 (0.5-18.6) years. Estimated 2-yr EFS was 72.0% ± 6.0 in ALL, and 62.4% ± 6.0 in AML patients. TRM in the whole cohort was 11.0% ± 2.6, incidence of aGvHD III-IV at 6 months was 12.3% ± 2.7, extensive chronic GvHD at 2-yr was 6.4% ± 2.1. Minimal residual disease-positivity prior to HCT was associated with higher CIR, both in ALL and AML. CloFluBu showed limited toxicity and encouraging EFS. CloFluBu is a potentially less toxic alternative to conventional conditioning regimens. Randomized prospective studies are needed.