Patients undergoing allogenic hematopoietic stem cell transplantation (HSCT) are at an increased risk of mortality due to transplant-related complications in the first year following transplantation, in part due to the profound immune dysregulation with T- and B-cell lymphopenia and functional impairment. Although several large studies have described higher mortality rates from the coronavirus disease 2019 (COVID-19) in HSCT recipients, no reports have focused on the impact of early COVID-19 infection on immune reconstitution post-transplant and correlation with transplant outcomes. We retrospectively analyzed 61 consecutive adult patients who underwent their first allogeneic HSCT at our institution. Thirteen patients (21.3%) experienced early COVID-19 infection with a median time to diagnosis of 100 days. In multivariable analysis, patients with early COVID-19 infection had significantly worse overall survival (adjusted hazard ratio [aHR], 4.06; 95% CI, 1.26 to 13.05; P=.019) and progression-free survival (aHR, 6.68; 95% CI, 2.11 to 21.11; P=.001).This was mainly attributed to higher non-relapse mortality (NRM) among early COVID(+) patients (P=.042). Allogeneic HSCT patients with early COVID-19 infection had significant delays in absolute lymphocyte count (95% CI, -703.69 to -56.79; P=.021), CD3+CD4+ (95% CI, -105.35 to -11.59; P=.042), CD3+CD8+ (95% CI, -324.55 to -57.13; P=.038), and CD3-CD56+ (95% CI, -193.51 to -47.31; P=.014) recovery compared to those without early COVID-19 infection. Our findings suggest that patients with early COVID-19 infection after allogeneic HSCT have higher NRM and worse survival, at least in part due to impairment in immune reconstitution post-transplantation.