With the aid of a special chair designed to allow him to practice hitting balls while recovering from knee surgery, he returned to competitive tennis in September 1989.

[2] Muster's comeback continued in 1990, when he won three top-level tournaments on clay (including the Italian Open, defeating Andrés Gómez in the semifinals and Andrei Chesnokov in the final) and one title on hardcourt.

Muster reached the semifinals of the 1990 French Open, losing in straight sets to the eventual champion, Andrés Gómez.

He also helped Austria reach the semifinals of the Davis Cup, where they were eliminated 3–2 by the United States, despite winning both of his singles rubbers against Michael Chang and Andre Agassi.

At the 1994 French Open, he won his second round match against Andre Agassi in five sets but was then defeated by the serve-and-volley play of Patrick Rafter in the next round, with Rafter's four set victory denying Muster a match against the reigning French Open champion Sergi Bruguera.

In March 1994, he defeated Michael Stich of Germany in a first round Davis Cup tie in Graz, 6–4, 6–7, 4–6, 6–3, 12–10, after saving a match point when trailing at 7–8 in the fifth set.

Despite Muster's win over Stich bringing Austria level at 2–2 in the tie, it was Germany who eventually won the decisive fifth rubber.

At the 1995 French Open, Muster won his first and only Grand Slam singles title, defeating Yevgeny Kafelnikov in the semifinals and comfortably beating 1989 champion Michael Chang in the final.

Muster was the only Austrian to win a Grand Slam singles title until Dominic Thiem won the 2020 US Open.

Although his record on other surfaces was less impressive, a late season victory over Pete Sampras on fast indoor carpet during his run to the title of the 1995 Eurocard Open (October) – Singles Masters event in Essen, Germany, gave Muster an outside chance at finishing the year no.

Despite Muster's continued dominance on clay-courts in 1996, he was upset in the Round of 16 at the 1996 French Open, losing to eventual finalist Michael Stich in four sets.

In July 1996, in the final of the 1996 Mercedes Cup in Stuttgart, Muster defeated newly crowned French Open champion Yevgeny Kafelnikov in three straight sets.

The validity of Muster's number one ranking was called into question by top Americans Pete Sampras and Andre Agassi, who argued that he had achieved the top spot based almost solely on his clay court results, although Muster had beaten Sampras on indoor carpet at the 1995 Masters event in Essen, Germany, and Agassi had only won tournaments on hardcourt in 1995.

After a semifinal victory over Jim Courier—his third successive win over the American in early 1997—Muster defeated Sergi Bruguera in three straight sets in the final.

In August 1997, Muster made a hard-fought run to the championship round of the Cincinnati Masters before losing the final to Sampras.

Having reached the semifinals or better in four of the five most important hard court events of the season to date, Muster was one of the favorites at the 1997 US Open – Men's singles.

However, as the fifth seed, Muster received a difficult first round draw and fell in four sets to Great Britain's Tim Henman, then ranked world no.

A strong run to the semifinals on the hard courts of Indian Wells—where he beat top-ranked Sampras along the way—in March 1998 buoyed Muster onto the European clay.

In his next event and first clay appearance of 1998, Muster reached the last top-level tournament final of his career in Estoril, losing to Alberto Berasategui in three sets.

In early May 1998, Muster defeated sixth-ranked Yevgeny Kafelnikov en route to the quarterfinals of the 1998 ATP German Open in Hamburg, Germany.

Muster's 1998 results faded after the spring, and he reached just one semifinal (Mallorca) and one quarterfinal (Boston) for the remainder of the year.

Following his first-round loss to Nicolás Lapentti at the 1999 French Open, Muster quietly disappeared from the ATP Tour at the age of 31.

After he stopped playing tennis after the 1999 French Open, Muster moved to Noosa Heads, Australia, where he had officially resided since 1996, and married television presenter Jo Beth Taylor in 2000.

On 13 September 2011, Muster won a second match after his comeback, in the Todi Challenger, against the fifth seeded Argentinian Leonardo Mayer.