"This is a very personal issue with him," Khan told USA Today after Wednesday's owners meetings concluded in New York regarding Trump's insistence that the league's players should all stand during the national anthem.
Trump attempted to buy the Buffalo Bills in 2014, but his bid failed. Khan believes that might be fueling the President's unrelenting criticism of the widespread player protests during the anthem this season.
"He's been elected President, where maybe a great goal he had in life to own an NFL team is not very likely," Khan told the newspaper. "So to make it tougher, or to hurt the league, it's very calculated."
Khan was one of seven NFL owners who made financial contributions to Trump, donating $1 million to his inaguration fund. Khan said he does not regret making the donation.
On Wednesday, Trump wrote two separate posts on Twitter criticizing the NFL, one of which said there has been "too much talk, not enough action" on the protests from the league.
Another tweet read, "The NFL has decided that it will not force players to stand for the playing of our National Anthem. Total disrespect for our great country!"
NFL commissioner Roger Goodell said Wednesday that the league's owners believe players should stand for the anthem, but the league has not changed its policy on the matter.
Goodell and a number of players, owners and Players Association representatives met earlier in the week to discuss the reasons behind the ongoing protests.