On June 25, 2016, after Brazilian wrestler Zumbi was not able to participate in the Cruiserweight Classic, WWE announced that Mustafa Ali would replace him. On July 20, Ali was eliminated from the tournament by Lince Dorado in the first round. Ali appeared on the October 26 episode of NXT, where he and Dorado entered the Dusty Rhodes Tag Team Classic, but were eliminated by Kota Ibushi and TJ Perkins in the first round.
On the December 13 episode of 205 Live, Ali made his cruiserweight division debut, wrestling Lince Dorado to a double countout. On January 23, 2017, Ali made his Raw debut, teaming with TJ Perkins and Jack Gallagher, defeating Drew Gulak, Tony Nese and Ariya Daivari. Ali began feuding with Drew Gulak, when Gulak began his "no fly zone" campaign on 205 Live. The feud culminated in a two-out-of-three falls match on July 18, which Ali won. In February 2018, Ali began participating in the Cruiserweight Championship tournament; he defeated Gentleman Jack Gallagher in the first round, Buddy Murphy in the quarterfinals, and Drew Gulak in the semi-finals to advance to the finals on the WrestleMania 34 kickoff on April 8, where he lost to Cedric Alexander. In June, Ali started a rivalry with Hideo Itami, who interfered in his him against Buddy Murphy. This resulted in a triple threat match between them on the June 19 episode of 205 Live, which Itami won after pinning Ali. On the July 3 episode of 205 Live, Ali defeated Murphy in a No Disqualification match. On the August 7 episode of 205 Live, Ali lost a match to Itami and collapsed afterwards, rendering him out of action for a short time. Ali returned after a month on the September 25 episode of 205 Live, where he wrestled Itami to a double countout before defeating him in a Falls Count Anywhere match on the October 23 episode of 205 Live to end the feud. The following week, Ali defeated Tony Nese to become the number one contender for the Cruiserweight Championship, but was defeated by champion Buddy Murphy at Survivor Series.
During his time in 205 Live, Ali gained the attention of WWE Chairman Vince McMahon, who decided to put him on the SmackDown brand. Ali made his first appearance on the December 11, 2018 episode of SmackDown Live, confronting WWE Champion Daniel Bryan. Later that night, Ali faced Bryan, but was defeated. The following week on SmackDown Live, Ali was confirmed as a full-time SmackDown roster member and teamed with AJ Styles to defeat Daniel Bryan and Andrade "Cien" Almas in a tag team match after Ali pinned Bryan. The following week, Ali defeated Almas. At the 2019 Royal Rumble, Ali competed in the eponymous match, lasting 30 minutes and eliminating Shinsuke Nakamura and Samoa Joe before being eliminated by Nia Jax.
Ali was scheduled to compete in the Elimination Chamber match for the WWE Championship at the Elimination Chamber event in February, which would have been his first world title match; however, he was pulled out due to a legit injury, and replaced by Kofi Kingston. Ali returned to competition at a WWE live event on March 2, and made his televised return at the Fastlane pay-per-view, as a last minute addition in a match between Kevin Owens and Daniel Bryan. Ali lost after he was pinned by Bryan. On March 25, 2019, Mustafa Ali's ring name was shortened to Ali. On the April 30 episode of SmackDown, it was announced that Ali would participate in the 2019 Money in the Bank ladder match, which he failed to win, after a returning Brock Lesnar interfered. The following month, Ali would compete in the 51-man battle royal at Super Showdown, but would fail to win. On July 27 at WWE Smackville, he was defeated by Shinsuke Nakamura in a match for the Intercontinental Championship. In August, Ali competed in the 2019 King of the Ring tournament where he defeated Buddy Murphy in the first round but lost to Elias in the quarterfinals. On the September 17 episode of SmackDown Live, Ali would rekindle his feud with Shinsuke Nakamura after Nakamura attacked him before their scheduled match. At the Hell in a Cell event, Ali would lose a match to Randy Orton. On November 13, 2019, Ali's name was reverted back to Mustafa Ali. At Survivor Series, Ali competed as a member of Team SmackDown, and was eliminated by Seth Rollins; however, his team won the match. Following this, Ali would be taken off television, wrestling primarily on dark matches and live events.
After a seven-month hiatus from television, Ali returned on the July 20, 2020 episode of Raw, teaming with Cedric Alexander and Ricochet to defeat MVP, Bobby Lashley, and Shelton Benjamin, thus moving to the Raw brand. After moving to the Raw brand, Ali later began competing on WWE Main Event, trading victories in matches over the likes of Ricochet and Akira Tozawa. On the September 28 episode of Raw, Ali would return to in-ring action by teaming with Ricochet and Apollo Crews, where they would go on to defeat The Hurt Business after Ali used the 450 splash to pin MVP.
On the October 5 episode of Raw, Ali was revealed as the leader of the stable Retribution after he ordered them to attack The Hurt Business during his match with MVP, thus turning heel for the first time in his career. On the October 19 episode of Raw, Ali would reveal himself as the mysterious hacker that was sending messages on SmackDown for months. That same night, Ali and Retribution would be defeated by The Hurt Business in an eight-man tag team match. The following week on Raw, Retribution would once again lose to The Hurt Business in a elimination match, ending the feud. Following this, Retribution would set their sights on Ricochet, with each member, including Ali, defeating him in singles matches over the next few weeks on Raw. Afterwards, Retribution would begin a feud with The New Day, or more specifically, Kofi Kingston after Ali blamed Kingston for "stealing" his WrestleMania opportunity two years prior while he was injured. At the Royal Rumble, Ali would enter at number four and managed to eliminate Xavier Woods before being eliminated by Big E. On the March 15, 2021 episode of Raw, Ali was defeated by Riddle to retain his United States Championship, then lost to him again in a rematch on the Fastlane kick-off show. Following the match, Reckoning and Slapjack walked out on him while Mace and T-Bar attacked him, effectively disbanding Retribution.
On the March 29 episode of Raw, in his first match since the disbandment of Retribution, Ali attacked Drew McIntyre after his match with Ricochet, resulting in a match against McIntyre, who emerged victorious. Shortly afterwards, Ali renewed his rivalry with Ricochet on Main Event, where they faced off in a series of matches culminating in a 2-out-of-3 falls match, where Ali was defeated. In June, Ali began a storyline with Mansoor, leading to a match on the July 5 episode of Raw, where Ali handed Mansoor his first pinfall loss after outsmarting him by faking a knee injury. On the July 26 episode of Raw, Ali teamed with Mansoor at his request, where they defeated T-Bar and Mace. As part of the 2021 Draft, Ali was drafted to the SmackDown brand. On the October 11 episode of Raw, Ali attacked Mansoor backstage after they lost to The Hurt Business, turning heel once again and thus ending his alliance with Mansoor, as well as challenging him to a match at Crown Jewel later that night. At the event, Ali lost to Mansoor, and after the match, was dropped with a kick by karate silver medalist Tareg Hamdi. The following night on SmackDown, Ali faced Mansoor in a rematch but was once again defeated. On the next week's episode of SmackDown, Ali would be defeated by Drew McIntyre and shortly after would disappear from television.
Ali returned to television on the April 25, 2022 episode of Raw, as a face, and defeated The Miz. After the match, he would be attacked by Tommaso Ciampa. On the May 2 episode of Raw, Mustafa Ali yet again interrupted Miz TV and requested a United States Championship shot. The Miz accepted the offer but turned the match into a two-on-one handicap match with The Miz's partner being Theory. Ali was defeated by a Skull Crushing Finale by The Miz. Eventually, however, Ali would face Theory for the United States Championship at Hell in a Cell, in an unsuccessful attempt. On the October 17 episode of Raw, Ali confronted Seth Rollins and unleashed an attack on him to end the episode.
Heading into 2023, Ali started a program with Dolph Ziggler, with the two confronting each other backstage on several occasions. On the February 20, 2023 episode of Raw, Ali defeated Ziggler with a roll-up and sarcastically celebrated his win. On the May 15 episode of Raw, Ali won a number one contender's battle royal to face Intercontinental Champion Gunther at Night of Champions, but was unsuccessful at the event. Ali made a surprise return on the May 30 episode of NXT, appearing in the crowd just before North American Champion Wes Lee and Tyler Bate teamed up against The Dyad (Jagger Reid and Rip Fowler). Ali later helped Lee and Bate fend off Joe Gacy. At NXT The Great American Bash on July 30, Ali was unsuccessful in capturing the NXT North American Championship against Lee and defending champion Dominik Mysterio in a triple threat match after interference from Mysterio's Judgment Day stablemate, Rhea Ripley. On September 21, nine days before he was scheduled to challenge Dominik Mysterio for the NXT North American Championship at NXT No Mercy, Ali was released from his WWE contract.