Lemon was one of three moderators at the debate.
"What do you say to those Trump voters who prioritize the economy over the president's bigotry?" he asked at one point.
The clip was shared by political strategist Caleb Hull.
At another point, Lemon said that Trump was racist without using the word "alleged." He did not provide evidence for the claim.
Trump took to Twitter Wednesday to hit back: "CNN’s Don Lemon, the dumbest man on television, insinuated last night while asking a debate 'question' that I was a racist, when in fact I am 'the least racist person in the world.'"
"Perhaps someone should explain to Don that he is supposed to be neutral, unbiased & fair ... or is he too dumb (stupid} to understand that. No wonder CNN’s ratings (MSNBC’s also) have gone down the tubes - and will stay there until they bring credibility back to the newsroom. Don’t hold your breath!" the president added.
Lemon has come under fire in the past for incendiary comments, such as claiming, "The biggest terror threat in this country is white men."
Like fellow CNN host Chris Cuomo, Lemon has defended the violent far-left extremist group, Antifa, and he has also regularly called Trump names, including "dummy."
The conservative watchdog, Media Research Center, released a video before the debate noting Lemon appears to have a "clear bias and hatred of conservatives and President Trump."
Trump later added his analysis of the debate in another missive, writing: "If I hadn’t won the 2016 Election, we would be in a Great Recession/Depression right now," he wrote.
"The people I saw on stage last night, & you can add in Sleepy Joe, Harris, & the rest, will lead us into an economic sinkhole the likes of which we have never seen before. With me, only up!"
He also shared a quote by close ally Sen. John Kennedy (R-La.): "The lesser of two Socialists is still a Socialist!"