Abstract Aim COVID-19 associated coagulopathy is widely documented in severe COVID-19 infection and COVID-19 Vaccine-Induced Thrombotic Thrombocytopaenia. However, much of this evidence relates to macrovascular thrombosis with limited evidence on the impact of previous mild, asymptomatic COVID-19 infection, or vaccination on microvascular thrombosis in free tissue transfer. We compared the rate of thrombotic complications in traumatic lower limb injuries requiring free flap reconstruction in the pre- and post-COVID era. Method Adult patients undergoing lower limb free flap reconstruction were identified at a single centre over two three-month periods (2019 and 2021). Standard thromboprophylaxis was used for all patients (intraoperative intermittent pressure devices, post-operative thromboembolic deterrent stockings, and prophylactic low molecular weight heparin until discharge). Thrombotic complications were recorded and compared using a chi-squared test. Results In the pre-COVID cohort, 51 patients underwent 52 free flaps. One flap (1.9%) suffered anastomotic thrombosis resulting in flap compromise. Post-COVID, 39 patients underwent 43 free flaps. Nine flaps suffered anastomotic thrombosis (21%) and one patient suffered a pulmonary embolus. This increase was statistically significant (p = 0.002). In the post-COVID cohort, four patients had a COVID-19 infection and 25 patients (64%) had at least one dose of a COVID-19 vaccine before free flap surgery. No patients had an active COVID-19 infection on admission. Conclusions In the post-COVID era there was an increased rate of thrombotic complications in lower limb free flap patients. Further research is required to delineate the best course of action when planning free tissue transfer for patients who have had previous COVID-19 infection or vaccination.