He published the earliest printed book of organ music in Germany and is grouped among the composers known as the Colorists.
According to the preface of his 1571 publication of organ tablature he traveled to foreign lands to study, but he gave no specifics.
Ammerbach developed a method of music notation for keyboard playing, known as tablature, which was specifically adapted for organ.
His method became known as the "new German organ tablature" and involved letter notation for the pitches with rhythmic symbols placed above.
His publications of music in tablature include arrangements of numerous composers popular in the mid-16th century, including Ludwig Senfl, Heinrich Isaac, Josquin des Prez, Clemens non Papa, Orlande de Lassus, and others; Lassus is particularly well represented, as can be expected both because of his extraordinary fame and his presence in Germany (he was in Munich between 1563 and 1594).