The couple, who were married for 22 years, spent the better part of a year dodging rumors that their relationship was on the rocks, but when Kris answered reader questions for PEOPLE in July, she put a mostly positive spin on things.
Admitting that she and the former Olympian, 63, weren't living together all the time, the 57-year-old responded with a firm "No!" when asked if they were getting divorced, insisting that they had "a pretty fabulous relationship."
"We were lucky enough to get a place by the beach [in Malibu]," she said. "[Bruce] spends time there back and forth. We all do. I don't have a crystal ball, but I hope we'll be old and gray together."
So what went wrong?
Bruce's Daughter: 'He's Doing Fine'"I think this is a decision that they have not come to lightly," Cassandra Marino, Bruce's daughter from his first marriage, tells PEOPLE.
The 33-year-old, who saw her dad at her daughter's birthday party a week or two ago, says "it was time for them to move on," and now that the split is public, "I wouldn't say that he's happier. I would just say he's doing fine."
A source close to the family tells PEOPLE that despite Kris's recent denials, "If you watch [Keeping Up With the Kardashians], it was pretty clear where things were headed."
When they wed, Bruce was the star in the family – a world-famous athlete who won gold in the decathlon at the 1976 Olympics – but after they scored a reality show in 2007 (on the heels of Kim Kardashian's sex tape), momager Kris took the lead in the relationship and, says the source, "Bruce lost his voice and his opinion with Kris."
"Sometimes he would mention that it bothered him, but most of the time he wouldn't say anything, so Kris just went about living how she was and treating him that way," the source admits.
As the manager of her older daughters, Kourtney, Kim and Khloé, Kris focused more on their careers and cashing in on their time in the spotlight, and "it took a toll on their relationship."
As the years rolled by, the couple drifted further and further apart, and "everyone from [their daughters] Kendall and Kylie, to [Kris's son] Rob and the girls, were well aware of the issues they were having," the source explains.
'Kris Runs the Show'A source at the reality show adds, "Kris runs the show, that's for sure. Bruce basically had no say in anything. He was told what to do. You'd go over [to their house] and there were always a million people running around, and it was pretty obvious Bruce didn't feel comfortable in his own house anymore. Half the time Kris would just shut him right down like she didn't want to hear from him."
The show source also says, "Bruce just wanted some peace and simplicity in their lives. They've become far from it. It's not that he doesn't appreciate what they have [in terms of money], but he didn't feel the need to always have more, like Kris did."
By the time Kim and her boyfriend, Kanye West, moved into the Jenners' Hidden Hills home with their new baby, North, in June, Bruce wasn't even around.
"This summer when the family got the Malibu house and Bruce called it 'his place' and he started staying there more than Hidden Hills, sure, the kids asked what was up," the source says. And Kris and Bruce "were honest."
In a joint statement on Tuesday the couple announced their separation and confirmed that they were living separately. "We are much happier this way," the pair told E! News in a joint statement. "But we will always have much love and respect for each other. Even though we are separated, we will always remain best friends and, as always, our family will remain our number one priority."
The source says that the couple, who haven't yet filed divorce papers, remain in constant contact with each other. "They talk every day," the source says. "It's just one of those things where they were happier with a little space between them than being together. There was no smoking gun or straw that broke the camel's back. Over the past few months they were just moving towards this and finally decided to acknowledge it."
Reporting by JENNIFER GARCIA, AILI NAHAS and RAHA LEWIS