Praetorius studied with his organist father, Jacob Praetorius, and with other figures in Hamburg and Cologne in the mid-1570s. His first church job was as organist at Erfurt from 1580 to 1582; he gave up this position to assist his father at Hamburg's Jacobikirche, and upon his father's death in 1586 he was named the church's first organist. He held this job for the rest of his life.
Almost all of his sacred choral music was published after he turned 50, although it is likely that he had been working on the scores for many years. He specialized in parody masses, based on motets, and wrote more than 100 motets of his own (including a few secular wedding motets). About half of these motets are polychoral works for two to four groups of singers, and mimic the progressive Venetian style of the time, with rich contrasts of texture and harmony, and quite active rhythm. He also produced several impressive eight-voice Magnificats.
In 1587, long before he had his own music published, Praetorius copied and disseminated to Hamburg churches a collection of monophonic German and Latin sacred music; he followed this up in 1604 with a collection of four-part German chorale settings by four Hamburg organists (including himself). This second collection is historically important as the first such German publication to call for organ accompaniment of chorales sung by congregations.
The only organ works definitely attributed to Praetorius are some full-textured Magnificat settings and a couple of chorales. Most of these Magnificat settings were composed by 1611 and included in the Visby Tablature, a collection that also includes many anonymous hymns, sequences, and Mass movements that are likely also Praetorius' work.