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Mask wearing and physical distancing are effective at preventing COVID-19 transmission. Little is known about the practice of these behaviors during physical activity (PA). In this longitudinal study, direct observation was used to describe COVID-19 prevention behaviors among physically active individuals. The Viral Transmission Scan (VT-Scan) was used to assess COVID-19 prevention behaviors of people standing, sitting, walking, jogging, and cycling in educational, retail, and residential areas. The VT-Scan was performed once per week over 22 weeks between 11:00 a.m. and 2:30 p.m. Information was manually extracted from videos collected during VT-Scans. A total of 4153 people were described, of which 71.2% were physically active, 80.0% were 18–30 years of age, 14.0% were non-white, 61.0% were female, and were 19.6% obese. Individuals not engaged in PA were less compliant with COVID-19 prevention behaviors than physically active people. Compliance differed by PA type, with walkers less compliant with COVID-19 prevention behaviors than joggers and cyclists. Among those physically active, non-compliance with COVID-19 prevention behaviors was higher in 18–30-year-olds, whites, and men. Engagement in COVID-19 prevention behaviors varies as a function of PA. Efforts to promote compliance with recommendations may benefit from tailored messaging, taking into account PA participation, PA type, and characteristics of physically active individuals.