Linke was remembered as a hard-nosed tackler with tremendous heading ability, and played in 13 Bundesliga seasons in representation of Schalke 04 and Bayern Munich, totalling 340 games.

He quickly earned his way into the starting line-up and, from 1992 until 1998, appeared in a total of 175 Bundesliga games for the Royal Blues, his debut coming on 1 September 1992 in a 0–0 home draw against SV Werder Bremen.

In his first season, he scored his first goal for the Bavarians in a 3–1 derby home win over TSV 1860 München on 7 November, but would also start in the notorious UEFA Champions League final against Manchester United.

Not until his last year, under coach Felix Magath, did he end up losing his starting role to Croatian Robert Kovač, appearing in only 11 games but helping in another league conquest.

During his second season, he added one last piece of silverware to his extensive collection by winning the league; on 3 May 2007, the club informed him that his initial two-year contract would not be extended.

After numerous injuries to the defensive line, national coach Jürgen Klinsmann personally called the player on the telephone and asked him to temporarily come out of retirement.