Multiparameter flow cytometry (MFC) measurable residual disease (MRD) before allogeneic hematopoietic cell transplantation (HCT) independently predicts poor outcomes in acute myeloid leukemia (AML). Conversely, its prognostic value in the newly defined disease entity, myelodysplastic neoplasm (MDS)/AML is unknown. To assess the relationship between disease type, pre‐HCT MRD, and post‐HCT outcomes, we retrospectively analyzed 1265 adults with MDS/AML (n = 151) or AML (n = 1114) who received a first allograft in first or second morphologic remission at a single institution between April 2006 and March 2023. At 3 years, relapse rates (29% for MDS/AML vs. 29% for AML, p = .98), relapse‐free survival (RFS; 50% vs. 55%, p = .22), overall survival (OS; 52% vs. 60%, p = .073), and non‐relapse mortality (22% vs. 16%, p = .14) were not statistically significantly different. However, a significant interaction was found between pre‐HCT MFC MRD and disease type (MDS/AML vs. AML) for relapse (p = .009), RFS (p = .011), and OS (p = .039). The interaction models indicated that the hazard ratios (HRs) for the association between pre‐HCT MRD and post‐HCT outcomes were lower in patients with MDS/AML (for relapse: HR = 1.75 [0.97–3.15] in MDS/AML vs. 4.13 [3.31–5.16] in AML; for RFS: HR = 1.58 [1.02–2.45] vs. 2.98 [2.48–3.58]; for OS: HR = 1.50 [0.96–2.35] vs. 2.52 [2.09–3.06]). On the other hand, residual cytogenetic abnormalities at the time of HCT were equally informative in MDS/AML as in AML patients. Our data indicate that MFC‐based pre‐HCT MRD testing, but not testing for residual cytogenetic abnormalities, is less informative for MDS/AML than AML patients when used for prognostication of post‐HCT outcomes.