The departure of Ferguson for Manchester United in November 1986 left the Dons board with the arduous task of replacing the irreplaceable, and they opted for little-known coach Ian Porterfield, who had achieved success in England with Sheffield United, but was untested at the top level. Porterfield's reign was not successful and ended with his resignation in May 1988.
Alex Smith and Jocky Scott formed a co-managership of the club to replace Porterfield, and achieved a League Cup and Scottish Cup double in 1989–90. In the 1990–91 season a run of twelve victories in thirteen games left Aberdeen sitting top of the table on goal difference ahead of Rangers, going into the final match of the season at Ibrox. A change of tactics (which eventually led to Jocky Scott leaving the club) and a Mark Hateley double gave the Championship to Rangers, and allowed them to continue on the Championship run that saw them eventually lift nine consecutive titles.
Alex Smith was not successful as manager in his own right, and was eventually sacked in 1992. Former captain Willie Miller took over and presided over two seasons where Rangers were run close, but chose at the end of the 1993–94 season to break up his team and bring in new players, a move which did not work; Miller was sacked before the end of the season, and the club had to rely on a play-off victory over Dunfermline Athletic to retain their Premier League status.
Miller was replaced by Roy Aitken, but his initial success in avoiding relegation did not last, and despite a League Cup win against Dundee in 1995–96, the club continued to struggle. Alex Miller and Paul Hegarty had spells in charge in the late 1990s, but success remained elusive, and with the financial burden of a new stand putting the club into debt for the first time in its history, the directors turned to Stewart Milne, a local businessman whose firm had built the stand, to bring business acumen to the running of the club.
The Danish-born Ebbe Skovdahl became Aberdeen's first non-Scottish manager in 1999, and his time in charge coincided with some of the heaviest defeats in the club's history, together with the first time the club had ever finished bottom of the league – the ensuing relegation play-off with Falkirk being avoided as Falkirk did not have a ground which met Premier League standards. Skovdahl did, however, lead the club to two cup finals in 2000 and a fourth-place finish in 2002, but left the club partway through the 2002–03 season when he felt he had taken it as far as he could.
Big things were expected from his replacement, Steve Paterson, who was regarded as a promising up-and-coming manager, and he led the club to a decent seventh-place finish that season. However, Paterson's first (and only) full season in charge, 2003–04, proved an absolute disaster as the club were threatened with relegation, only managing to escape due to Partick Thistle being even worse, and Paterson was sacked after a five-game losing streak at the end of the season. Jimmy Calderwood took over as manager in 2004, having been identified as the right man for the job by the newly appointed Director of Football, former player and manager Willie Miller.
Aberdeen under Calderwood have posted more consistent results than in previous seasons; fourth in season 2004–05 and 6th in season 2005–06, but the club are not yet challenging for major honours in the way they did in the second half of the 20th century. In season 2006–07, despite being knocked out of both cups in the earlier rounds, the club finished in third place in the SPL and qualified for the 2007–08 UEFA Cup with a comfortable 2–0 victory over Rangers at Pittodrie on the last day of the season.
In September 2007, Aberdeen created club history by defeating Dnipro on the away goals rule in the UEFA Cup, the first time the club had won on the away goals rule in 40 years of European football. In the group stage, despite failing to win their first three matches, the combination of other results meant Aberdeen could progress with a home win over Danish champions FC København – they achieved this in style, winning 4–0 (biggest margin of victory since the 80s, before one of Pittodrie's biggest crowds since the 80s) to set up a February 2008 meeting with German giants (and 1983 throwbacks) Bayern Munich.
In May 2009, having secured a 4th-place finish in the Scottish Premier League and a return to European competition, Jimmy Calderwood left his position as manager of Aberdeen by 'mutual consent'.
Calderwood was replaced by former player Mark McGhee. McGhee's time at Aberdeen was not successful. A few weeks after a club record 0–9 defeat to Celtic, McGhee was sacked in December 2010 and replaced by Craig Brown.
Aberdeen failed to produce better results under Craig Brown's tenure, and in March 2013 he announced his retirement to take up a non-executive director role on the club's board