In the 1999–2000 season, Faber suffered new injuries on his hamstring, Achilles tendon and ankle. In February, he underwent an operation on his ankle, which had to be put in a cast. PSV won the Eredivisie that year, but Faber only appeared in three league matches. In the build-up to the 2000–01 season, PSV won the Johan Cruyff Shield after beating Roda JC with 2–0. Faber scored the second goal in the match. After the match, Faber ended up with an injured left knee. When a few weeks of rest did not solve the troubles, an operation followed in September. PSV clinched the league title again and this time Faber had a bigger contribution with 17 matches. In June 2001, Faber extended his contract with PSV for another two years. In the following two seasons, Faber played 42 Eredivisie matches and won his fourth league title in 2003, but was still struggling with his injuries. In the 2001–02 season, Faber received a head wound in the match against Heerenveen and suffered a minor knee injury. Newcastle United showed interest in signing him in early 2002, but after the new injury a possible deal was cancelled.