Manchester United and Bayern Munich had only met twice in competitive matches before the final, both meetings coming earlier in the 1998–99 season and both finished as draws. Manchester United's only other German opponents in their history were Borussia Dortmund, against whom they had an overall winning record, with three wins, two defeats and a draw in their six matches, including a 10–1 aggregate win in the second round of the 1964–65 Inter-Cities Fairs Cup and a 2–0 aggregate defeat in the 1996–97 UEFA Champions League semi-finals. Bayern Munich had an equally narrow advantage in their 22 matches against English opposition, with seven wins, nine draws and six defeats, including a win over Leeds United in the 1975 European Cup Final and a defeat to Aston Villa in the 1982 final.
Including the victory over Leeds in 1975, Bayern Munich had won the European Cup on three occasions going into the 1999 final. With three victories in a row from 1974 to 1976, they became only the third team to achieve such a feat after Real Madrid (1956 to 1960) and Ajax (1971 to 1973). They had also finished as runners-up twice: in 1982 against Aston Villa and 1987 against Porto. Although Bayern had been waiting 23 years for a European Cup title, Manchester United had had to wait even longer, their only victory having come in 1968. Their manager then was Matt Busby, who had been seriously injured in the Munich air disaster, which killed eight of his players on the way back from a European Cup tie in Belgrade 10 years earlier, before rebuilding the team to become European Cup winners. Busby died in 1994; the day of the 1999 Champions League final would have been his 90th birthday.
Although it was the second Champions League season to feature clubs that had not won their national leagues the year before, Manchester United and Bayern Munich were the first such clubs to reach the final of the competition. Nevertheless, both went into the match as champions, having won their domestic leagues in 1998–99; Bayern Munich claimed the Bundesliga title with a 1–1 draw against Hertha BSC on 9 May with three games to go, while Manchester United left it until the last day of the season (16 May), when they came back from 1–0 down against Tottenham Hotspur to win 2–1 and beat Arsenal to the title by a point. Both teams were also playing for the ; in addition to their league win, Manchester United had beaten Newcastle United in the 1999 FA Cup Final on 22 May to claim the , while Bayern were due to play Werder Bremen in the 1999 DFB-Pokal Final on 12 June.