In this prospective study, the authors aimed to identify the existence of potential brain microstructural changes related to SARS-CoV-2 infection. Diffusion tensor imaging (DTI) and 3D high-resolution T1WI sequences were acquired in 60 recovered COVID-19 patients and 39 age and sex-matched non-COVID-19 controls. Registered fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) were quantified using DTI, and an index score system was introduced. Regional volumes derived from Voxel-based Morphometry (VBM) and DTI metrics were compared using analysis of covariance (ANCOVA). Two sample t-tests and Spearman correlation were conducted to assess the relationships among imaging indices, index scores and clinical information. They found that COVID-19 patients had statistically significantly higher bilateral grey matter volumes (GMV) in olfactory cortices, hippocampi, insulas, left Rolandic operculum, left Heschl’s gyrus and right cingulate gyrus and a general decline of MD, AD, RD accompanied with an increase of FA in white matter, especially AD in the right CR, EC and SFF, and MD in SFF compared with non-COVID-19 volunteers (corrected p value <0.05). Global GMV, GMVs in left Rolandic operculum, right cingulate, bilateral hippocampi, left Heschl’s gyrus, and Global MD of WM were found to correlate with memory loss (p value <0.05). GMVs in the right cingulate gyrus and left hippocampus were related to olfactory loss (p value <0.05). MD-GM score, global GMV, and GMV in right cingulate gyrus were correlated with lactate dehydrogenase level (p value <0.05). The authors concluded that this study reveals the possible disruption to microstructural and functional brain integrity in the recovery stages of COVID-19, suggesting long-term consequences of SARS-CoV-2. https://doi.org/10.1016/j.eclinm.2020.100484