Purpose Available clinical data have revealed that coronavirus disease 2019 (COVID-19) is associated with a risk of pulmonary microthrombosis and small airway disease. These patients present with varying degrees of perfusion abnormalities. The purpose of this study was to evaluate the use of a ventilation/perfusion single-photon emission computed tomography/computed tomography (VQ SPECT/CT) in the detection and follow-up of persistent lung perfusion abnormalities that were suspected to be due to pulmonary microthrombosis, small airway disease, or both. Methods A retrospective study was conducted at the department of nuclear medicine of Universitas Academic Hospital in Bloemfontein, South Africa. We reviewed the studies of 78 non-hospitalized patients with COVID-19 infection referred to our department from July 2020 to June 2021 for a perfusion only SPECT/CT study or a VQ SPECT/CT study. Pulmonary embolism was suspected in all 78 cases. Results Seventy-eight patients were studied. The median (interquartile range) age was 45 (41–58) years, and the majority ( n = 69; 88.5%) were females. Twenty-two (28.2%) of these patients had matching VQ defects with mosaic attenuation on CT. All nine of the patients who had follow-up studies had these abnormalities persistently, even after 1 year. Conclusion We confirm that the VQ scan is a safe and effective tool to identify and follow-up recovered COVID-19 patients with persistent ventilation and perfusion abnormalities suspicious of small airway disease and pulmonary microthrombosis.