On 9 May 2013, Manchester United announced Everton manager David Moyes would replace Ferguson as the club manager from 1 July, having signed a six-year contract. He ended the following season by winning his 12th and Manchester United's 19th league title and thus overtaking Liverpool's record of 18. However, he refused to end his boycott and Manchester United said they would pay the resulting fines.

In March 2021, he added that when he was signed, a Rangers director had questioned whether the Fergusons had been married in a (Catholic) chapel, and that the director had replied "oh, that's okay" when told they had married in a registry office. The season did not go especially well, with Aberdeen reaching the semi-final of the Scottish Cup and the Scottish League Cup Final, but losing both matches and finishing fourth in the league.The absence of Ferdinand hampered United's defence of the Premier League in the 2003–04 season; the team finished third behind Arsenal's " Invincibles" and Chelsea. In Ferguson's final match in charge, Manchester United drew 5–5 at West Bromwich Albion, a hat-trick from Romelu Lukaku, later a United player, denying Ferguson a final victory. Analyst Alan Hansen stated that he believed Ferguson was "the key component" in United's success that season, so key in fact that "[he] would have claimed the crown with any of the other top sides had he been in charge of them". Keane headed in a Beckham cross to halve the deficit just before half-time, but was later shown a yellow card for a foul on Edgar Davids, which prevented him from playing in the final.

After a sub-standard start to the 1983–84 season, Aberdeen's form improved and the team won the Scottish league and retained the Scottish Cup. The 1991–92 season did not live up to Ferguson's expectations and, in Ferguson's words, "many in the media felt that [his] mistakes had contributed to the misery". Ferguson was on a part-time contract with St Johnstone, and he combined working in a Govan shipyard with training at night in Perth. Originally started as an amateur venture, Seagull Books has quickly grown into a knowledgable and reputable on-line book vendor. The majority of pages are undamaged with some creasing or tearing, and pencil underlining of text, but this is minimal.However, another run of disappointing results in the final quarter of the season saw them fall down to mid-table.

Many of Ferguson's former players have gone on to become football managers themselves, including Tony Fitzpatrick, Alex McLeish, Gordon Strachan, Mark McGhee, Willie Miller, Neale Cooper, Bryan Gunn, Eric Black, Billy Stark, Bryan Robson, Steve Bruce, Mark Hughes, Roy Keane, Paul Ince, Chris Casper, Mark Robins, Darren Ferguson, Ole Gunnar Solskjær, Henning Berg, Andrei Kanchelskis, Michael Appleton, Ryan Giggs, David Healy, Gabriel Heinze, Paul Scholes, Gary Neville, Jaap Stam, Michael Carrick, Wayne Rooney and Phil Neville. The season began well with a 4–1 win over defending champions Arsenal on the opening day, but United's league form quickly turned sour. He was counter-accused of intimidating behaviour towards his office secretary because he wanted players to get some expenses tax free.Winning the title ended United's 26-year wait for a league title, and also made them the first Premier League champions. In the January transfer window, Serbian defender Nemanja Vidić and French full-back Patrice Evra were signed, and the side finished in second place in the league, behind runaway winners Chelsea. On 23 December 2006, Cristiano Ronaldo scored the club's 2,000th goal under Ferguson in a match against Aston Villa. He did not speak to her for six weeks, confiscated her keys and communicated only through a 17-year-old assistant. Ferguson is the longest-serving manager of Manchester United, having overtaken Sir Matt Busby's record on 19 December 2010.