Both of them suffered from substance abuse -- Bono to pain killers and Elia to alcohol -- but Elia decided to stay with her partner as he began taking testosterone and their relationship was severely tested.
"Hormones change people and I think he's leveled out right now," she said. "There was a period where I felt they were kind of spiked. The testosterone was like really machismo, and it was hard to deal with."
Elia added that she had a rough time living through and seeing Bono change from Chastity to Chaz.
"There is a softness that is gone for sure," she said. "Literally at that point when I was watching the female essence leave his body, it was hard."
But an added benefit of the hormone injections, the couple said, is that the testosterone has improved their sex life.
"[It's] just a higher sex drive, like all men," Bono said. "It is different."
"It's more intimate. It's more personal," Elia said. "And it's more frequent."
It was after Bono underwent surgery to have his breasts removed that Elia said she had a realization about the person Chaz wanted to be.
"I was terrified to see what the results were going to look like," she said. "When it did happen and I saw the reveal, I had a relief go through me. I was like, 'Oh, so this is how you're supposed to look. OK, now it all makes sense.'"
Ecstatic about having the surgery, Bono said he hated his breasts from the moment they developed and that he has felt much better since having them removed.
"I never wear a shirt at home anymore, ever," he said.
Anatomically, Bono remains a woman from the waist down and said he doesn't have any plans to undergo corrective surgery yet because that type of surgery is still risky.
"I'm just kind of waiting to see what happens and hoping that there are medical advances made and it gets a little better because right now the risk-reward ratio is just not quite right," he said. "The majority of [transgender people] don't have bottom surgery because of that."
But even without physically having a penis, Bono said he has always felt like a man, long before taking hormone injections.
"That's not to say I wouldn't like a penis," he said. "I really would like one and I hope that someday I will get one."
His partner also said she completely views Bono now as a male. "I don't even think of him at all as a woman. I haven't for years," Elia said.
Since the transition, Bono said he's the same person he's always been, but just in a different body.
"I am the male version of my former self," he said.
In an exclusive interview with "Nightline" anchor Cynthia McFadden last year, Cher talked about some of the concerns that she had about Chaz transitioning.
"I was really frightened in the beginning, and also, I felt that the doctors did not do their due diligence," Cher said at the time, adding that she also supported Chaz and his decision.
"I have two sons," Cher said in the interview. "Never thought that would be, but, you know, you go through life and you get what you get."
Bono said that his relationship with his mother continues to "move in the right direction."
Bono was first introduced to the public on his parents' popular '70s television series, "The Sonny & Cher Comedy Hour." Often seen wearing frilly dresses and shiny shoes on the show, Bono said that even when he was a little girl, he was friends with and liked to dress like boys.
"My seventh and eighth grade year was a particularly hellacious year for me," he said. "Puberty. And I was at a school that just wasn't appropriate for my needs. It was just very straight, strict academic school."