On July 19, 2016, at the 2016 WWE draft, Bray Wyatt and Erick Rowan were drafted to SmackDown while Braun Strowman was drafted to Raw, separating him from the group. On the August 16 episode of SmackDown Live, Wyatt walked away from Rowan after the latter lost his match against Dean Ambrose, leaving Rowan's sheep mask on Wyatt's rocking chair. Despite this, Rowan attacked Randy Orton on behalf of Wyatt on the September 13 episode of SmackDown Live, continuing their alliance. On October 9, Luke Harper returned at the close of the SmackDown brand's No Mercy event on October 9 in a match between Wyatt and Orton, whom Harper distracted to help Wyatt win the match, thus realigning himself with Wyatt. Prior to Harper's return, Rowan underwent surgery to repair a torn rotator cuff and would be out of action for four to six months.
On the October 25 episode of SmackDown Live, Orton interfered on Wyatt's behalf in his match against Kane. On the November 1 episode of SmackDown Live, Wyatt and Harper helped Orton win in his respective match against Kane, thus confirming his allegiance to the group. At the thirtieth annual Survivor Series on November 20, Wyatt and Orton were the sole survivors for Team SmackDown in the traditional 5-on-5 Survivor Series elimination match after Orton saved Wyatt from a spear from Roman Reigns. On the November 29 episode of SmackDown Live, Wyatt and Orton defeated American Alpha to become the number one contenders for the SmackDown Tag Team Championship. They went on to challenge and defeat Heath Slater and Rhyno on December 4 at TLC: Tables, Ladders, & Chairs for the tag team titles, Wyatt Family's first championship in WWE's main roster. While Wyatt and Orton retained the SmackDown Tag Team Championship against the former champions on the December 6 episode of SmackDown Live, it was announced that the Wyatt Family invoked the Freebird Rule and thus allowing Harper to also defend the championship.
On the December 27 episode of SmackDown Live, the Wyatt Family began to show tension after they lost the SmackDown Tag Team Championship to American Alpha in a four-way elimination tag team match after Orton inadvertently hit Harper and was subsequently pinned. On the January 10, 2017 episode of SmackDown Live, they unsuccessfully attempted to regain the championship after another miscue between Orton and Harper, who accidentally performed a superkick on Wyatt after the match, resulting in Wyatt walking away in frustration. This continued the following week on SmackDown Live, when Orton lost to Ambrose after Harper distracted his teammates, causing Orton and Harper getting involved in another argument, which would physically escalate until they were separated by Wyatt, who struck Harper, resulting in Harper walking away. On the January 24 episode of SmackDown Live, Orton defeated Harper after which Wyatt attacked Harper with a Sister Abigail, but did not dictate whether he was kicked out of the group.
During the Royal Rumble match on January 29, Harper attacked both Orton and Wyatt, even attempting Sister Abigail on the latter before being attacked by Orton, who would then go on to win the Royal Rumble match. At Elimination Chamber on February 12, Orton defeated Harper while in the main event Wyatt won the WWE Championship in the Elimination Chamber match. The following night on SmackDown Live, after Wyatt successfully defended the WWE Championship in a triple threat match involving John Cena and AJ Styles (despite a pre-match attack by Harper), Orton came to the ring, pledging allegiance to Wyatt and refusing to face him at WrestleMania 33. The following week on SmackDown Live, Wyatt gave Orton "the keys to the kingdom" which referred to the Wyatt Family's compound, but Orton turned on Wyatt by burning down the Wyatt Family compound on the February 28 episode of SmackDown Live before challenging him to a match at WrestleMania 33, seemingly disbanding the Wyatt Family in the process.