Training for the 2008–09 season began on 30 June 2008. Several players were still on vacation due to the Euro 2008 and Franck Ribéry was missing due to injury. After a 45-minute in-training test against their own amateurs, the first official test was won at SV Lippstadt 7–1. Further tests on 19 July in Nördlingen and 20 July in Amberg were won 8–0 and 11–1. The T-Home Supercup against Borussia Dortmund marked the first loss of the season (1–2). After a goalless draw at 1. FC Köln on 26 July Bayern went to Japan for a guestplay at Urawa Red Diamonds, beating the host 4–2. On 5 August Bayern hosted Internazionale in the Franz Beckenbauer Cup for the final test before the regular season and was defeated by Inter 1–0.
On 8 August Klinsmann announced that Mark van Bommel would succeed Oliver Kahn as captain. Two days later, in the first cup match, third league club Rot-Weiß Erfurt provided unexpected difficulties for the Bayern as the club went to catch up on a Bayern lead three times, before having to concede to Bayern's fourth goal. In the opening game of the Bundesliga season 2008–09 hosted Hamburg. As Hamburg caught up from two goals behind, the game ended 2–2, leaving HSV yet unbeaten in the Allianz-Arena. After another draw at Dortmund the succeeding week brought two squad changes for Munich as Jansen decided to leave Bayern for Hamburg and Massimo Oddo was loaned out from Milan. The first league victory followed against Berlin, 4–1.
On 4 October, Bayern drew level with VfL Bochum, despite leading 3–1 with just seven minutes left in regulation. However, goals in the 84th and 85th minutes saw Marcel Koller's men leave the Allianz with a point. A few days later Bayern lost a friendly at Ingolstadt 04 but proceeded to win all other games in the month, including the Champions League home game against Fiorentina.
On the 16th day of play, Bayern defeated current leader 1899 Hoffenheim, thus coming very close to the top of the standings. The final match of the Champions League group stage was also won at Lyon, completing Bayern's best performance in the group stage. A draw at VfB Stuttgart was Bayern's final game before the winter break. Coincidentally Stuttgart was also Bayern's first opponent after the break. While Bayern won this cup game 5–1 away the first league match was lost at Hamburg 0–1.
After winning at home against Borussia Dortmund, Bayern lost their next two games at Berlin, that thereby took the lead in the league, and at home against newly promoted Köln. A 5–0 victory in the Champions League at Sporting CP was the final game of the month.
After a draw in the league at Bremen Bayern was eliminated from the cup by Bayer Leverkusen. Munich won all other games in the month, including a 7–1 in the 2nd leg against Sporting, thus achieving a record aggregate of 12–1.
After 5–1 defeat in the league at Wolfsburg, a direct rival for the championship, Bayern suffered another severe loss (4–0) at the hands of FC Barcelona. Bayern held Barcelona to a draw in the second leg a week later but was elimininated from the competition nevertheless. In the league Munich managed to win against underdogs Frankfurt and Bielefeld, but a home defeat at the hands of Schalke led to the dismissal of coach Klinsmann. The club appointed Jupp Heynckes as caretaker coach and Hermann Gerland as assistant caretaker coach.
Bayern won their first three games under Heynckes as coach, defeating Mönchengladbach, Cottbus, and Leverkusen. A draw at Hoffenheim led to a delicate situation before the last game: Second-place Bayern hosted third-place Stuttgart. While the winner of the match would be qualified for the Champions League, and even win the championship if Wolfsburg lost, the loser would probably fall to the fourth place, thus not qualifying for the Champions League at all. As fourth-place Berlin lost and Wolfsburg won, the game eventually just decided that Bayern would go to the Champions League directly while Stuttgart would go to the qualification. The season concluded with four friendly games at Kaufbeuren, Eichstätt, Magdeburg, and Sittard, which Munich won all.
Bayern hosted Hamburg in the opener of the 46th Bundesliga season on 15 August 2008. On the last day of play on 23 May 2009 they won against Stuttgart, thus finishing second in the league. The second place qualified Bayern for the UEFA Champions League 2009–10.
In the first round of the cup Bayern faced Rot-Weiß Erfurt. The east Germans from the third tier were able to equalize three times before finally succumbing to Bayern. A victory at home against second-tier Nuremberg followed. In the third round Bayern managed one of their best performances of the season, winning 5–1 at Stuttgart, but they lost in the next round to Bayer Leverkusen.
Bayern's Champions League season started on 17 September at Bucharest. The other group rivals were Lyon and Fiorentina. They finished the group stage undefeated in first place and put away Sporting CP on a record margin in the first knockout round, but were not match for Barcelona in the quarter-final. Club officials spoke of a "massive humiliation" and being "taken apart" after the 0–4 in the first leg.
EU = if holds or not a European Union passport; Country: when 2 flags, 1st flag = country that plays for internationally, 2nd flag = country of birth; N = number on jersey; P = Position (for position name, pause mouse pointer on abbreviation); Name = Name on jersey (for more extensive name, pause mouse pointer on name); Age = age on the day of the signing; Moving from = only indicate the club the player was playing before start playing for this club in this season, for the type of the moving see Status column; Moving to = only indicates the club the player is going to play next, for the type of the moving see Status column; Ends = when the player's current contract ends; n/a = Not applicable.