Kris, 59, had visited her ex at her Malibu home on Tuesday for what marked the first meeting between the two since Caitlyn transitioned from a man to a woman.
The source told E! News that "everything is fine" between the former couple but that the meeting was needed. Caitlyn and Kris have not commented.
The two, who are parents to daughters Kendall Jenner, 19, and Kylie Jenner, 17, were married for 23 years and finalized their divorce late last year. They split in October 2013, more than a year and a half before the Olympian, formerly known as Bruce Jenner, revealed in a TV interview her plan to transition. She debuted her female look and new name in a Vanity Fair cover story and photo spread on June 1.
Kris was the last of the family members to see Caitlyn in women's clothes, following plastic surgery to make her look more feminine. The Keeping Up With the Kardashians momager had openly struggled with the news of her ex's transition, as seen on the show. After Caitlyn's Vanity Fair story and cover was released, she said, "I think that someone following their dream is truly inspirational to a lot of people."
Kris had also supported Caitlyn earlier this month after she debuted her female look in person in public for the first time at the 2015 ESPYs, where she gave a moving speech. Kris said Caitlyn looked "beautiful." She had also said weeks earlier that Caitlyn's Vanity Fair photos were "beautiful."
On the debut episode of Caitlyn's docu-series I Am Cait, which aired this past Sunday, Caitlyn was seen debuting her female look in person for the first time to Kylie (via FaceTime), her mother, Ester Jenner, 89, sisters Pam and Lisa and as well as Kim Kardashian's husband Kanye West, 38.
On Wednesday, a day after her meeting with Kris, Caitlyn was photographed leaving a restaurant and bar in West Hollywood, dressed in a white and black polka dot blouse and dark blue skinny jeans, after meeting up with friend Candis Cayne.
Also that day, she was seen wearing a strapless black jumpsuit and matching half-sleeve sweater while dining at Eva Longoria and JT Torregiani's restaurant Beso.
Caitlyn had until this week been photographed wearing mostly dresses and skirts in public. She wore a Versace dress similar to one once worn by Angelina Jolie at the ESPYs. On I Am Cait, she was seen showing Kim a black Tom Ford dress she had acquired. Kim told her Kris had the same one in chocolate brown and Caitlyn joked that they should stage a "Who Wore it Best?" prank.
Tune in to I Am Cait Sundays at 8 p.m., only on E!