Although the team had a slow start to the 2008–09 season,^[159] United won the Premier League with a game to spare,^[160] making Ferguson the first manager in the history of English football to win the Premier League three times consecutively, on two separate occasions. Ferguson had now won 11 league titles at Manchester United, and the 2008–09 season title success put them level with Liverpool as league champions on a record 18 occasions in total.^[161] They also won the Football League Cup on penalties after a goalless Wembley draw with Tottenham Hotspur.^[162]

They contested the 2009 Champions League final against FC Barcelona on 27 May 2009 but lost 2–0.^[163][164]

After the presentation ceremony, Ferguson conceded that he would stay on at United for as long as his health permitted him and that he would be glad to win the league title once more. This would make United's total league wins one more than rivals Liverpool, becoming the outright leader in total wins.^[165]

In 2009–10, Ferguson added another Football League Cup to his honours list as United defeated Aston Villa 2–1 in the Wembley final on 28 February 2010.^[166]However, his dreams of a third European Cup were ended a few weeks later when United were edged out of the competition in the quarter-finals by Bayern Munich on away goals. And their hopes of a record 19th league title were ended on the last day of the season when Chelsea beat them to the Premier League title, crushing Wigan Athletic 8–0 and rendering United's 4–0 win over Stoke City meaningless.

On 8 August 2010, Ferguson added another FA Community Shield to his honours list as United defeated Chelsea 3–1 in the final in Wembley. On 19 December 2010, Ferguson became Manchester United's longest serving manager in history, overtaking Matt Busby's record of 24 years, 1-month and 13 days in charge of the club.^[167] He ended the season by winning his 12th and Manchester United's 19th league title and thus overtaking Liverpool's record of 18. Manchester United faced Barcelona again on 28 May 2011 in the 2011 UEFA Champions League Final, their third in four years, but United lost 3–1. 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".^[168] With Edwin van der Sar, Gary Neville and Paul Scholes all retiring in 2011,^[169] Ferguson spent big by signing defender Phil Jones from Blackburn Rovers and winger Ashley Young from Aston Villa for around £17 million each,^[170][171] and goalkeeper David de Gea from Atlético Madrid for around £19 million.^[172]

On 2 September 2012, Ferguson managed his 1000th league game with United against Southampton. United won the game 3–2 thanks to a hat-trick from Robin Van Persie. Two weeks later, he won his 100th game in the Champions League with a 1–0 win over Galatasaray at Old Trafford.