Greg Glassman stepped down after athletes, gyms and sportswear firms cut ties with his $4bn (£3.1bn) brand.
Mr Glassman acknowledged having caused a "rift" in the CrossFit community.
His exit came on the day of Floyd's funeral in Texas. The unarmed black man died last month after a policeman in Minneapolis knelt on his neck.
CrossFit is a branded exercise regimen that involves high-intensity group workouts with a focus on strength and conditioning. Gyms around the world offer classes.
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