Course of the season
After the sacking of coach Jürgen Klinsmann late in the previous season, Jupp Heynckes had taken over as caretaker coach until the end of the season. It was thus that Bayern had to find a replacement in the summer break. Their choice fell on the Dutch Louis van Gaal, who had just led AZ Alkmaar to a championship in his home country. The signing of Van Gaal was in stark contrast to the signing of Klinsmann before the previous season, as Klinsmann came with absolutely no experience at the club level while Van Gaal had been working as a coach in club football for almost 20 years. His quality as a coach was further underlined by the titles he had already won.
Before Van Gaal's arrival, the club had already signed Mario Gómez for a Bundesliga record sum of €35 million, as well as Anatoliy Tymoshchuk, Ivica Olić and Alexander Baumjohann. Finally, Andreas Görlitz returned on loan from Karlsruher SC. Van Gaal then encouraged the recruitment of Danijel Pranjić and Edson Braafheid. On the outgoing side, the loanee Massimo Oddo returned to Milan, Tim Borowski was sold to his former club Werder Bremen, Lúcio left for Inter Milan after many successful years with the Reds, and Zé Roberto signed with Hamburger SV when he could not agree with Bayern on a new contract.
The pre-season began with a score of friendlies which had been arranged still under the reign of Klinsmann. While Van Gaal was not happy with the packed schedule, as he preferred to work with the team, Bayern played a mostly successful preseason, including several high wins against opponents from lower tiers. They also managed to win in their own Audi Cup for which they had invited international premier clubs Milan, Manchester United, and Boca Juniors. Van Gaal waited until after the last friendly to decide on two key roles in his team. In the previous season, Klinsmann had first chosen Michael Rensing as keeper of choice, but in the second half of the season, he switched to Hans-Jörg Butt after a string of unsatisfactory games. The other important issue was that of the team captain and his replacements. On the day prior to the first competitive game of the season, the cup match at Neckarelz, the coach announced his decisions. Mark van Bommel stayed captain and Philipp Lahm became his first replacement. Van Gaal had also announced that the keeper he elected for the Neckarelz game would be his keeper of choice for the season, and in the cup game, it was Rensing who had the starting position as goalkeeper.
In their first game, Bayern did not shine, but put away the underdogs from Neckarelz 3–1. The first games in the league were draws against 1899 Hoffenheim and Werder Bremen, before Bayern lost their first game to newly promoted Mainz 05. Just before the next Bundesliga match, Bayern announced that they had signed Arjen Robben in a last minute transfer from Real Madrid. In his first game, against VfL Wolfsburg a day later, Robben scored twice, but after a string of victories, including a 3–0 victory away at Maccabi Haifa in the starter of the Champions League, Bayern began to struggle. A loss at Hamburger SV and a draw at home against 1. FC Köln saw the Reds to the eighth place in the league, marking the worst start in decades, and the media already speculated about an even quicker sacking of Van Gaal than that of Klinsmann the previous season.
Although the draw at Köln would eventually be the start of a series of 19 undefeated games in the league, Bayern won only two of their next five league games, drawing the other three. Meanwhile, they lost twice to Bordeaux in the Champions League. This led to a configuration where Bayern could not make it to the knockout phase without the help of Bordeaux. As Bordeaux already secured qualification to the knockout phase, many expected that they would not put all their effort into their next match against Juventus, and a win of the Italians would mean the end of Bayern's Champions League campaign this season.
The Reds won their last four league matches before the winter break, and also managed to win at Haifa while Bordeaux indeed defeated Juventus, meaning that Bayern and Juventus decided who qualified for the next round face to face in the final match of the group stage. The Germans needed to win, while the Italians would be through with a draw. When David Trezeguet put Juventus in front in the 19th minute, prospects looked bleak for Bayern, but they managed to turn the game around and eventually won 4–1.
January – May
After the winter break, Bayern won game after game. Five in the league completed a streak of nine consecutive victories while Fiorentina was put away 2–1 in the first leg of the Champions League round of 16, and second-tier SpVgg Greuther Fürth was run over 6–2 in the cup.
On 20 February 1. FC Nürnberg managed a draw against Bayern, thus ending their streak of victories, but on the following day of play a victory of the Reds at Hamburg saw them to the top of the standings for the first time in more than 18 months. A draw at Cologne and a victory against SC Freiburg completed Bayern's streak of 19 undefeated games in the league. On 9 March at Fiorentina, the club also reached the next round of the Champions League although their first loss after the winter break, 3–2, meant that they advanced only on the away goals rule.
Despite a loss at Eintracht Frankfurt on 20 March, Bayern stayed in first place, but that was of minor importance as the deciding weeks were yet to come. Within three weeks Bayern was to play in the semi-final of the cup against Schalke 04, in the league against their direct rivals, Schalke and Leverkusen, and the best team in the second leg of the league, VfB Stuttgart. In the Champions League the club faced Manchester. Bayern won the first of the matches at Schalke, the cup semi-final, in a close game after extra time. Three days later a loss at home against Stuttgart set the Reds back into second place in the league. Yet another three days later Bayern won the first leg of their quarter-final encounter with Manchester United. For the next game the club returned to Schalke where they won again, thus reclaiming their lead in the league. In the second leg the quarter-final at Manchester Bayern was down by two early, but managed to get back into the game. Eventually they won by the same score as in the previous round, 2–1 and 2–3, to advance to the semi-final. The final game of these weeks was their away game at Leverkusen where the Reds were able to claim a draw.
Next Hannover 96 was stomped 7–0, but otherwise the Reds did not have time to take breath. The first game of their semi-final against Lyon was a heated affair with red cards on both sides, but Bayern emerged victorious. Before going to Lyon for the second leg, Bayern had to face their classic rival, Mönchengladbach, in the league. A 1–1 let Bayern stay ahead of Schalke. Then the game at Lyon was all Ivica Olić's. The Croat put three past Lyon and Bayern advanced to their first Champions League final since their triumph in 2001.
With only four games left Bayern could still win the Treble, but they had not claimed a single title yet. On 1 May, Bayern defeated VfL Bochum in the league, thus putting the title out of Schalke's reach. Officially Bayern were not champions yet, but even if Schalke won on the last day while Bayern lost they would still have to do that by a result that was by 17 goals better than Bayern's. Unsurprisingly, the title went to Munich as Bayern won their last game whereas Schalke didn't. A week later Bayern faced another of their continuous rivals, Werder Bremen, in the cup final. The result was one of the most lopsided in the history of German cup finals as the Reds won 4–0. Only the most prestigious title was elusive as Bayern could not overcome Inter in the final of the Champions League.
Bayern had no post-season friendlies this year, but eleven players where internationals of teams that had qualified for the 2010 FIFA World Cup. Franck Ribéry joined the French World Cup squad, Martín Demichelis the Argentinian. Arjen Robben and Mark van Bommel were part of the Dutch squad and seven players, Butt, Lahm, Badstuber, Schweinsteiger, Klose, Müller, and Gómez, were called up for Germany. Butt replaced Adler who missed due to injury. Lahm became captain of the team as Ballack also missed the tournament due to injury.