Chimeric antigen receptor-transduced T (CAR-T) cell therapy is an effective cell therapy against advanced hematological tumors. However, the use of autologous T cells limits its timely and universal generation. Allogeneic CAR-T cell therapy may be a good alternative as a ready-to-use therapeutic. Graft-versus-host disease (GVHD) is an obstacle for allogeneic CAR-T cells, but can be prevented by TCR deletion through genome editing. However, the remaining TCR-positive cells must be eliminated by costly, large-scale magnetic cell separation. Therefore, an alternative method for removing TCR-positive cells is needed. In this study, we found that monovalent anti-CD3 Abs such as Fab and single-chain variable fragment (scFv), but not whole IgG, induce apoptosis of in vitro expanded T cells, thereby effectively depleting residual TCR-positive T cells during TCR-deleted CAR-T cell generation and ultimately preventing xenogeneic GVHD in vivo. Thus, monovalent anti-CD3 treatment during allogeneic CAR-T cell manufacturing would be an efficient method to prevent GVHD.