Primary refractory acute myeloid leukemia (prAML) is a poor prognosis disease, with allogeneic hematopoietic stem cell transplantation (allo-HSCT) being the only potentially curative option. We retrospectively evaluated outcomes in 1574 adult prAML patients who underwent allo-HSCT from matched sibling donors (MSD), 10/10 or 9/10 unrelated donors (UD), or haploidentical donors between 2015 and 2020. Median follow-up was 24, 30, 38, and 24 months for MSD, UD 10/10, UD 9/10, and haploidentical transplants, respectively. MSD recipients were younger (median age 53 vs. 58–59 years in other groups, p < 0.001), had better performance status, and proceeded to transplant more quickly (3.8 months vs. >4 months in other groups, p = 0.004). In multivariate analysis, haploidentical HSCT was associated with inferior leukemia-free survival (LFS) and overall survival (OS) compared to other donor types. Additional negative predictors included adverse cytogenetics and longer time from diagnosis to transplant. Conversely, reduced-intensity conditioning and good performance status of the patient were associated with improved LFS. Disease progression remained the leading cause of transplant failure, underscoring the urgent need for more effective early post-transplant strategies.