Evidence has shown increased morbidity and mortality for patients with COVID-19 infection within 7 weeks of surgery. However, no studies have specifically investigated the effects of COVID-19 in microsurgical outcomes. This study evaluated thrombotic and overall complications after free tissue transfer for a variety of indications in patients with and without previous COVID-19 infection. A retrospective cohort study was performed in adult patients with or without a history of COVID-19 infection who underwent microsurgical reconstruction between 2017 and 2022. Patients with a history of COVID-19 infection were matched to controls based on age, gender, race, body mass index, history of diabetes, coronary artery disease, hypertension, Caprini score, tobacco use, and flap indication. From 2017 to 2022, 35 patients had a documented history of COVID-19. Matched case analysis determined a 4.8 times increased odds ratio of postoperative complications in the COVID-19 group compared with controls (p = 0.002). Significantly, more patients with COVID-19 experienced total or partial flap loss and anastomotic issues (COVID-19: 7/35, Control: 0/35; p < 0.001). There was no significant difference in incidence of VTE (COVID-19: 1/35, Control: 0/35; p = 0.493). Of note, 62.9% of the COVID-19 group were discharged on anticoagulants (versus 14.3% in the control group [p < 0.001]). COVID-19 has dire, long-lasting effects on virtually every organ system, chief among them, the microcirculation. Further studies are needed to fully determine the extent and influence of COVID-19 on complex procedures such as free tissue transfer and how to optimize the screening, workup, and postoperative care to guard against the associated thrombotic consequences.