As a guest conductor, Matthias Beckert directs, amongst others, the Hof Symphony Orchestra, Jena Philharmonic Orchestra, the Nuremberg Symphony Orchestra, Thüringen Philharmonie Gotha, the Thuringian Symphony Orchestra Saalfeld-Rudolstadt and the Vogtland Philharmonic Orchestra.

He has successfully worked with early music ensembles such as the Akademie für Alte Musik Berlin, the Concert Royal Cologne and the Würzburg Baroque Orchestra.

From 1999 to 2005 he conducted the Pizzicato Orchestra. Furthermore, he founded the Mainphilharmonie, with whom he carries out extraordinary projects of the Monteverdi Choir Würzburg and performs demanding oratorio works.