In one radio interview from 2019, Macgregor criticized the Clinton administration's involvement in the Kosovo War conflict in the late 1990s as an attempt to "essentially cultivate friendship and understanding in the Muslim world" by intervening against the Serbian forces.
"So we intervened against the Orthodox Serbs, Orthodox Christian Serbs in Kosovo and put essentially a Muslim drug mafia in charge of that country and called it a great success story for democracy," said Macgregor, appearing to side with the Serbians. "These people have never been our friends. They aren't ever going to be our friends. They are incurably hostile. I'm talking about the Sunni Islamists."
The US involvement in Kosovo successfully fought against Serbian forces, who are estimated to have
ethnically cleansed at least 11,000 people and displaced more than 1.5 million Kosovar Albanians.
According to Macgregor's biography, he was responsible for the strategic planning that led to the Kosovo Air Campaign and was later promoted to supervise the conduct and planning of operations on the strategic level with a staff of 240 officers and noncommissioned officers from 19 NATO nations until the end of the Kosovo War.