Matteo Messori was born in Bologna where he studied Organ and Counterpoint, graduating cum laude. He studied Harpsichord with the harpsichordist, organist, conductor and singer Sergio Vartolo at the Conservatories of Mantua and Venice, graduating again cum laude.
In addition, he studied Musicology at the University of his native city.

He is active as both a harpsichord and organ soloist and conductor in Italy, Europe and America, and also works with various chamber ensembles.

As means of exploring the musical and cultural relationship between the Italian penisula and the northern musical world in the sixteenth to eighteenth centuries, Messori founded the ensemble "Cappella Augustana", which he is conducting in the first complete recording of Heinrich Schütz' works for Brilliant Classics (Vols. 1-4, 19 CDs).
He also directed, for the Swedish label Mvsica Rediviva, the first sound tribute wholly dedicated to the sacred music by the Kapellmeister in Dresden and organist at the Thomaskirche in Leipzig, Vincenzo Albrici (1631-1690/96).

He has recorded the third part of the Clavierübung by Johann Sebastian Bach on three historical central German organs ("5 de Diapason", March 2008).
In June 2008 he recorded Die Kunst der Fuge, Musikalisches Opfer and the fragmentary Triple Fugue BWV 1080/19 by J. S. Bach, as a soloist on three several harpsichords (also in Central German style, with 16'-stop), as well as a leader of the ensemble "Cappella Augustana". The 3-CDs box contains also the Canonical Variations, recorded on the Trost organ of Walthershausen, 1724.

He regularly conducts orchestras and ensembles in Europe (a.o. Capella Cracoviensis, State Chamber Orchestra of the Republic of Belarus, the first Italian stage performance of the Händel oratorio La Bellezza ravveduta with Cappella Augustana).

In the Bach-Jahrbuch 2010 he has published a study of the 16' harpsichord with pedal harpsichord built by Zacharias Hildebrandt for the Collegium Musicum in Leipzig.

He teaches at the Bergamo Conservatory.