Scientists studied people who were discharged from the JR Hospital between March and May.
The C-MORE study found many coronavirus survivors are still suffering from breathlessness, fatigue, anxiety and depression months later.
The Oxford team also found abnormalities on MRI in multiple organs and persistent inflammation.
The study is being led by researchers from the university's Radcliffe Department of Medicine and involved 58 patients with moderate to severe laboratory-confirmed COVID-19.
The team also recruited 30 uninfected controls from the community.
The participants underwent magnetic resonance imaging (MRI) of their brain, lungs, heart, liver and kidneys; spirometry to test their lung function; a six-minute walk test; cardiopulmonary exercise test (CPET), as well as assessments of their quality of life, cognitive and mental health.
Two to three months after the onset of the disease, 64% of patients experienced persistent breathlessness and 55% complained of significant fatigue.
On MRI, tissue signal abnormalities were seen in the lungs of 60% of the COVID-19 patients, in the kidneys of 29%, in the hearts of 26%, and the livers of 10%. Organ abnormalities were seen even in patients who had not been critically ill when admitted.
MRI also detected tissue changes in parts of the brain, and patients demonstrated impaired cognitive performance. Their ability to sustain exercise was also significantly reduced, although this was due to a combination of fatigue and lung abnormalities.
The study also found that patients were more likely to report symptoms of anxiety and depression, and a significant impairment in their quality of life compared to the controls.
Dr Betty Raman, who is leading the C-MORE study along with Professor Stefan Neubauer, said: "Our study assessed patients recovering from COVID-19 following hospitalisation, two to three months from disease onset. Whilst we have found abnormalities in multiple organs, it is difficult to know how much of this was pre-existing and how much has been caused by COVID-19.
"However, it is interesting to see that the abnormalities detected on MRI and exercise capacity in patients strongly correlated with serum markers of inflammation. This suggests a potential link between chronic inflammation and ongoing organ damage among survivors."