But on Sunday night, fans of the famous clan learned that her concern had less to do with Jenner's desire to become a woman than it does with how he's handled telling his children.
"I've always been defending you and protecting you," Khloe said in the first part of the "Keeping Up with the Kardashians" special "About Bruce."
When Jenner told Khloe and daughter Kendall that he's probably going to completely say goodbye to himself as Bruce by the spring, Khloe said she wants him to be happy but is frustrated with his timing.
"I don't think it's fair you don't tell us how close this is. We are still your kids," she said.
The emotional special, which included sit-down interviews with five of Bruce Jenner's children and ex-wife Kris Jenner, also showed home movies of the family through the years.
Though there were a lot of tears shed -- by everyone -- during the hour, there were lots of happy moments and even some laughs.
Kris Jenner called her 25-year marriage to Bruce a "match made in heaven."
"We had so much in common," she said. "We went to races. We played golf. We went snow skiing. I mean, there wasn't anything we didn't do, and we could not keep our hands off each other."
Despite her own difficulties, Khloe even showed up to a meeting with her dad bearing "woman-friendly" gifts.
"I don't know her taste yet, so I'm trying to find that out," Khloe said.
Kim Kardashian revealed she's been keeping her stepdad's secret
for more than a decade, remembering walking in on him while he was dressed like a woman.
"I was hysterical," Kim remembered.
Kendall says she found lipstick and other makeup and thought her dad was having an affair with another woman.
But she said, "He's the most amazing person I know. I couldn't ask for a better dad," and it's clear Jenner shares those feelings, calling his children
his "greatest accomplishment."
Ahead of a sit down with all five of his reality-star daughters, Jenner told Kim
, "I'm so tired of lying about my life.
"I just want to be honest."
Yet during that family meeting, he admitted there's no guidebook for transitioning correctly and addressed Khloe directly, acknowledging he hasn't always gotten it right.
"If I'm not honest because I'm afraid to talk to you about this subject, because I know it hurts, I understand that," Jenner said. "Am I doing it right, Khloe? You can never do this right, OK? There's no right way to do this."
Part 2 of "Keeping Up With the Kardashians: About Bruce" airs today at 9 p.m. on E!