In 2009, Melzer again made a poor first quarter of the year, only managing one back-to-back win in his first ten tournaments, and it was at the 2009 Australian Open, where he reached the third round, losing to Andy Murray. It was not until the 2009 Internazionali BNL d'Italia that he recorded back-to-back wins, including a win over Nikolay Davydenko, but lost to Fernando González in the following round. He then reached the quarterfinals of the 2009 Interwetten Austrian Open Kitzbühel and the 2009 Gerry Weber Open once again, and the third round of the 2009 French Open and Wimbledon for the second year in a row. He reach his first semifinal of a year at the 2009 ATP Studena Croatia Open Umag, but lost to eventual champion Nikolay Davydenko. He also reached the quarterfinals of the 2009 Pilot Pen Tennis with a victory over Victor Hănescu, but lost in the following round to Fernando Verdasco. In the semifinal of 2009 PTT Thailand Open Melzer lost to eventual champion Gilles Simonin two sets. At the 2009 Shanghai ATP Masters 1000, Melzer defeated a then-world no. 5 Juan Martín del Potro, before losing to Feliciano López. This was his second victory over a top-5 player. The first was his win over a then-world no. 2 Tommy Haas in 2002. He ended 2009 on a high note by winning his second career title at the 2009 Bank Austria-TennisTrophy over Marin Čilić in straight sets, which included a victory over Radek Štěpánek in the quarterfinals.