He was principally active in Rome, in the service of the Papal Chapel, and was one of the judges at the famous debate between Nicola Vicentino and Vicente Lusitano in 1551.
In his manuscript treatise Sopra una differentia musicale sententiata he asserts that he was employed by Pierluigi Carafa, member of an aristocratic family in Naples.
In August 1565 he was forced to retire from the papal chapel as part of a reorganization and reduction in size which followed from the reforms of the Council of Trent.
An autograph manuscript source containing sacred music, like as a Salve Regina, a Magnificat, a Mass (Missa de Beata Virgine), some hymns and motets, probably composed by Danckerts, has recently come to light.
Artusi used portions of Danckerts' treatise in his reactionary 1600 publication Imperfettioni della musica moderna, which he wrote as an attack on Monteverdi.