The Bcl2 inhibitor Venetoclax (ven) in combination with 5-azacytidine (aza) has become increasingly used as an effective frontline therapy for treatment of high risk AML patients. Despite its efficacy in treating AML, patients often require haematopoietic stem and progenitor cell (HSPC) transplantation in order to achieve long term survival. Given that effective HSC engraftment and establishment of haematopoiesis are dependent on the bone marrow microenvironment (BME), this study utilised a multi-parameter approach to investigate the impact of ven/aza on the BM niche. Flow cytometry, Co-Detection by Indexing (CODEX) spatial imaging combined with single cell RNAseq (scRNAseq) analysis of isolated BME cells shows significant remodelling of the BM vasculature in response to two weeks of ven/aza treatment, including loss of sinusoidal endothelial cell (SEC) compartment leading to vascular leakiness. This was coupled with a break down in endothelial cell-cell interaction, and the downregulation of key niche factor genes in SECs important for HSPC homing and proliferation. Consequently, homing of human CD34+ was significantly compromised in mice treated with ven/aza prior to transplantation. Furthermore, engraftment of donor derived EPCR+ HSCs was dramatically decreased after 12 weeks post transplantation, showcasing the importance of the SEC compartment in the successful engraftment of long-term HSCs. Notably, ven/aza induced remodelling of the bone marrow vasculature is reversible, with full recovery of the SEC compartment observed 3 weeks post therapy. As a result, engraftment of EPCR+ HSCs was rescued in mice that were transplanted 3 weeks post ven/aza therapy. Hence for the first time, we have described the phenotypical and molecular impact of ven/aza therapy on the BM vascular niche and the negative impact this has on successful transplantation of donor derived long-term HSCs post therapy.