Allogeneic stem cell transplantation (allo-SCT) is a salvage treatment option for patients with relapsed or refractory lymphoid malignancies. However, the clinical variables impacting outcomes in these patients remain unclear. We analyzed 58 patients who underwent allo-SCT for lymphoid malignancies, including B-cell lymphoma (BCL, n = 20), Hodgkin's disease (n = 3), multiple myeloma (n = 9), natural killer/T-cell lymphoma (NK/TCL, n = 4), and TCL (n = 22). The median progression-free survival (PFS) was 27.4 months, while the median overall survival (OS) was 30.6 months. In univariate analysis, human leukocyte antigen (HLA) matching and complete remission status post-transplantation were associated with improved PFS and OS. However, only post-transplant response remained significant for both survival outcomes in the multivariate analysis. Moreover, HLA matching was associated with a significantly improved PFS in patients with BCL and NK/TCL, but with better OS only in those with BCL. Complete remission after transplantation was associated with better PFS and OS in patients with BCL, NK/TCL, and TCL. Our results indicate that post-transplant response is an important prognostic indicator in allo-SCT for lymphoid malignancies and may guide clinical decisions and additional treatment.