It was May 2019 and national security officials were in the Situation Room discussing Iran when President Trump abruptly changed the subject. He wanted to talk about granting asylum and citizenship to white South African farmers.

Mr. Trump had floated the idea before, claiming that the farmers were a persecuted minority group being displaced from their land, according to John R. Bolton, his national security adviser at the time, who was at the meeting.

Mr. Bolton said he thought little of Mr. Trump’s wish. The president had embraced fringe ideas and false narratives pushed by white Afrikaner activists, Mr. Bolton said.

“It never amounted to anything, so I just put it as typical Trump,” Mr. Bolton recalled in a recent interview. “Some random person tells him something and he’s obsessed with it.”

Five years later, Mr. Trump’s views on white farmers in South Africa are shaping U.S. foreign policy in his second term. On Monday, the first group of Afrikaners, a white ethnic minority that ruled during apartheid in South Africa, landed in Washington, as the Trump administration upended a refugee system that had provided sanctuary for those fleeing war, famine and natural disasters.

The administration is welcoming white South Africans after suspending the program for everyone else, including other Africans who have waited in refugee camps for years and were vetted and cleared, and Afghans who supported the U.S. war in their country.