At Hell in a Cell on October 30, Flair regained the title from Banks in the first ever women's Hell in a Cell match to become a three-time women's champion. This was also the first time a women's match was the last match on a WWE pay-per-view. The following night on Raw, Flair was revealed as captain of Team Raw for Survivor Series on November 20, where Team Raw defeated Team SmackDown with Flair and Bayley being the survivors for Team Raw. On the November 28 episode of Raw, Flair competed against Banks in a falls count anywhere match, where Banks defeated Flair for the title, after which Ric Flair came out and celebrated with Banks. A 30-minute iron man match between the two was scheduled for Roadblock: End of the Line on December 18, which resulted in a 2–2 draw, but Flair defeated Banks 3–2 in sudden death overtime, becoming a record four-time Raw Women's Champion as well as ending their six months feud since it was stipulated that Banks could not invoke her rematch clause after that. Shortly after, Flair started a feud with Bayley who managed to defeat her in two non-title matches since her main roster debut in August. This led to a title match between the two that took place at the Royal Rumble on January 29, 2017, where Flair successfully retained the title over Bayley.
On April 11, 2017, Flair was moved to SmackDown brand as part of the Superstar Shake-up. The following week on SmackDown Live, she defeated SmackDown Women's Champion Naomi in a non-title match, to earn a title opportunity, which ended in a no-contest after The Welcoming Committee (Natalya, Carmella and Tamina) attacked both contestants. This match made Flair the first woman in WWE history to ever compete in the main events of Raw, SmackDown and a WWE pay-per-view. In May, Flair aligned with Becky Lynch and Naomi against The Welcoming Committee, turning face in the process. At Backlash, The Welcoming Committee defeated Flair, Naomi and Lynch in a six-woman tag team match when the latter submitted to Natalya's sharpshooter. Shortly afterwards, Flair competed at Money in the Bank, as part of the first ever women's money in the bank ladder match, which was won by Carmella. On July 23, at Battleground, Flair competed in a five-way elimination match to determine the number one contender for the championship but was the last woman eliminated eventual winner Natalya.
Flair appeared in the January 2016 issue of Muscle & Fitness. Flair ranked 29th out of 50 in the 2017 Sports Illustrated fittest woman athletes of the year. In June 2018, Flair appeared in the ESPN Body 10 magazine.
In 2017, Flair portrayed Heather Rockrear in Psych: The Movie.
Flair released Second Nature: The Legacy of Ric Flair and the Rise of Charlotte, co-written with her father and Brian Shields, author of the WWE Encyclopedia. on September 19, 2017.