He spent the next couple of years back in Stuttgart's reserve team, and it wasn't until August 1994 that he made his third Bundesliga appearance, when he replaced Marc Kienle in a 2–2 draw with 1.

Over the next seven years he established himself as a regular member of Stuttgart's first-team, playing alongside experienced defenders such as Thomas Berthold, Zvonimir Soldo and Frank Verlaat, and such were his performances that he was almost called up to the Germany national team by then coach Berti Vogts.

In 1997 Stuttgart won the DFB-Pokal, and Schneider played in the final, replacing Matthias Hagner for the last 20 minutes of the victory over FC Energie Cottbus.

He spent two seasons with Hannover, and only made eight appearances, and was forced to retire early in the summer of 2005, due to illness brought on by a tick bite that had been spotted too late.

On 26 August 2013, Schneider became the head coach of VfB Stuttgart's first team, replacing Bruno Labbadia, who was on a 3-game losing streak.