Called Louis Theroux: Surviving America's Most Hated Family, he will explore the changes the family at the centre of the Westboro Baptist Church have gone through in recent years.
Theroux tweeted after the documentary aired on BBC2: "I know it may appear that I am "recruiting" for Westboro but that is emphatically not the case."
In an interview with Stylist, Theroux explained that he originally had no plan of covering the family for so long and didn't think a third film was necessary.
"I thought now we know each other's games, there is no need to really follow up a third time," he told the magazine.
Theroux resisted calls to look at the family again following the death of the church's founder and figurehead Pastor Fred Phelps, known as Gramps, in 2014.
But after he noticed a change in the group, he changed his mind.
"Enough time went by and I began seeing signs they were starting to change a little bit," he explained.
"Specifically, that this rather extraordinary ex-member called Megan Phelps was beginning to campaign in a very thoughtful and informed and sensitive way for tolerance and understanding.
"I felt it was a helpful way of looking at the nature of profound ideological disagreement."
Megan is the granddaughter of the late Pastor Phelps and has criticised the church.
"In a sense, it's a kind of version, I don't want to stretch this too far, but in its own way it's reminiscent of the Islamic State, this concept of radicalisation and de-radicalisation. To what extent can someone reform and change?
"And even in a less extreme way, in the world of Trump and the alt-right, how do you engage with people like that and change minds and change hearts. Or is it better just to turn away and have nothing to do with them?
"Those are the things I wanted to think about."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.