Born in Dresden, Eisenberg was organist at various churches beginning age nine. He was a member of the Dresdner Kreuzchor for five years. He studied in Leipzig at the Hochschule für Musik und Theater "Felix Mendelssohn Bartholdy" with Wolfgang Schetelich, completing the A-exam in 1978. During his studies, he was the winner of several international competitions, including the improvisation competition in Weimar. He won a prize of the International Johann Sebastian Bach Competition for organ in 1976.
In 1980, shortly before the completion of the new building of the Gewandhaus, Kurt Masur arranged for Eisenberg to be named organist of the Leipzig Gewandhausorchester. He also served as a harpsichordist of the Leipzig Bach Orchestra. He appeared on East German television in a production about the life of Johann Sebastian Bach. He appeared outside East Germany, in 1983 at the Bach Festival in Graz and in 1985 at the Internationale Bachakademie Stuttgart. In 1985 Eisenberg was a guest professor for organ at the International Music Seminar in Weimar. He also conducted master classes in Stockholm and Buenos Aires, among others.
In 1986 Eisenberg did not return from a tour to West Germany. After positions at churches in Bad Homburg and Hanover, he has performed as a freelance organist and harpsichordist and as a partner of chamber ensembles and symphony orchestras in cities across Europe, Asia, North and South America, and Australia. From 1992, Eisenberg was cantor at St. Severin in Westerland on Sylt. Since November 2004 he has been church musician and organist in Zwickau.
As an organ specialist, Eisenberg has been involved in numerous new organs and renovations. He recorded the complete Bach organ works in various organs in Lower Saxony. He has recorded as a partner of Mathias Schmutzler, Joachim Schäfer, and Giora Feidman, among others. Several of his CDs contain improvisations. As a conductor, he recorded Bach's secular cantata Mer hahn en neue Oberkeet, BWV 212 from the harpsichord, with soloists Juliane Claus, Martin Krumbiegel and Georg Christoph Biller in 1992, Bach's church cantata Ich armer Mensch, ich Sündenknecht, BWV 55 with Martin Petzold and members of the Thomanerchor in 1998, and songs from Schemellis Gesangbuch (Schemelli's Songbook) with Thomanerchor singers of two generations in 1998, playing the organ.
In 2003 Eisenberg was appointed Kirchenmusikdirektor (de) (church music director) in Hannover. Also in 2003, Schleswig-Holstein's Prime Minister Heide Simonis awarded him the honorary title of professor, for his outstanding contributions for organ music.
- "Matthias Eisenberg (Conductor, Organ, Harpsichord)". Bach Cantatas. Retrieved 8 April 2013.
- "Orgelmusik vom Feinsten mit Matthias Eisenberg" (in German). New Apostolic Church. 16 September 2012. Retrieved 19 April 2013.
- "Eisenberg, Matthias" (in German). kirchenmusikinhannover.de. Retrieved 19 April 2013.
- The first concert presented in the Third Gewandhaus was on 8 October 1981.
- Gerberding, Eva (September 2008). Sylt: 12 Highlights. Aktuelle Internet-Links. DuMont Reiseverlag. p. 55. ISBN 978-3-7701-6493-6.
- Hinse, Beate. "Organist Matthias Eisenberg wird mit dem Ehrentitel "Professor" ausgezeichnet" (in German). Schleswig-Holstein. Retrieved 18 April 2013.
- "Matthias Eisenberg" (in German). musiksommer-markranstaedt.de. 2007. Retrieved 23 April 2013.
- Kükenshöner, Christine (5 November 2009). "Trauriger Tröster auf der Orgelbank" (in German). Die Evangelische. Retrieved 19 April 2013.
- "Ironie, Pathos und Scherz Giora Feidman und Matthias Eisenberg im Kloster Eberbach" (in German). Frankfurter Allgemeine Zeitung. 8 August 2001. Retrieved 8 April 2013.
- Genossenschaft Deutscher Bühnen-Angehöriger; Deutscher Bühnenverein; Fachschaft Bühne (Reichstheaterkammer); Reichstheaterkammer (Germany). Präsident (2001). Deutsches Bühnen-Jahrbuch. Druck und Kommissionverlag F.A. Günther & Sohn. p. 186.
- Early Music Review. King's Music. 2002.
- Drouve, Andreas (2006). Publik-Forum. Herder. p. 27.
- "Matthias Eisenberg / Bach Cantatas". Bach Cantatas. 2006. Retrieved 23 April 2013.
- Matthias Eisenberg website (German)
- Literature by and about Matthias Eisenberg in the German National Library catalogue
- Matthias Eisenberg at AllMusic
- Matthias Eisenberg, Orgel musicontact