BACKGROUND: Physical activity (PA) is known to decrease COVID-19 risk factors and can attenuate symptoms of viral infections. However, difficulty exercising and fatigue are common complaints after COVID-19. It is unknown whether prior habitual PA will improve outcomes and what the time course is until full recovery of PA after COVID-19. METHODS: Invitations were emailed to 21,933 adults who were SARS-CoV-2 positive between March 2020 and February 2021. Participants completed intake surveys and the Physical Activity History (PAH) questionnaire regarding PA during the 3-month prior to infection. Monthly thereafter, for up to 23 months, participants were emailed surveys. Scores were computed for moderate and heavy PA. Long COVID (LC) was defined as having recurring/persistent symptoms 9 months after diagnosis. RESULTS: Overall, 993 patients completed the intake survey (age 50.7±15.8 years, BMI 27.3±9.2, 58% women); 28% had been hospitalized. One-third had recovered to their pre-infection level of PA at 9 months post-infection; this increased to 65% at one year, and 90% at two years. Higher pre-diagnosis PA reduced odds of hospitalization (P<0.05) but not of LC. Factors predictive of poor PA recovery were higher pre-diagnosis PA, shortness of breath and fatigue during acute illness, and fatigue chronically. Participants who reported ongoing symptoms had consistently poorer recovery of habitual PA compared to those not reporting chronic symptoms. CONCLUSIONS: Habitual PA reduced odds of hospitalization but not of LC. Thirty-five percent had not returned to pre-COVID-19 levels of PA one year after infection, representing a major public health threat.