Some Millwall supporters booed the players taking the knee ahead of their Championship game against Derby County on Saturday.
Fans of the club were returning to The Den for the first time since the outbreak of coronavirus, with 2,000 permitted in for the match versus the Rams due to the area being in Tier 2.
Players and staff of teams from all around the country have been taking the knee for months as a show of support for the Black Lives Matter movement.
But there was a vocal show of disapproval by a significant number of Millwall fans as it happened before them for the first time on Saturday.
Lions fans are among those allowed to return to watch their side with only clubs in Tier 3, the strictest coronavirus restrictions, prevented from doing so.
Any clubs in Tier 1 would be allowed to admit 4,000 spectators, but there are no professional sides in those few areas.
Fans returned at other EFL clubs in midweek including at Wycombe and Luton in the Championship.
Arsenal had 2,000 spectators in the Emirates for their Europa League clash against Rapid Vienna on Thursday, which was the first time fans had returned to a Premier League ground.