His first post may have been as maestro di cappella at Santa Maria dei Monti in 1588, and he is known to have acquired the post of maestro di cappella at San Luigi dei Francesi in Rome in 1591, after his brother left to join the papal choir.
Following the appointment at San Luigi dei Francesi, he was associated with Cardinal Montalto, a wealthy and influential patron of art and music, and may have served as teacher, composer, and archivist for the Cardinal at his church, San Lorenzo in Damaso.
Nanino's music of the 1580s and 1590s is conservative in idiom, avoiding the experimental tendencies of his brother and Marenzio, preferring instead to incorporate the technique and expressive style of the earlier Roman composers such as Palestrina.
After about 1610 he adopted the technique of basso continuo in his sacred works — hardly a conservative tendency — and, significantly, something his brother never did.
Much of his earlier music is secular (such as madrigals), but he published several books of motets after 1610, after his brother's death.