Praetorius was born Michael Schultze, Schultheis, or Schultz, the youngest son of a Lutheran pastor, in Creuzburg, in present-day Thuringia. After attending school in Torgau and Zerbst, he studied divinity and philosophy at the University of Frankfurt (Oder). He was fluent in a number of languages. After receiving his musical education, from 1587 he served as organist at the Marienkirche in Frankfurt. From 1592/3 he served at the court in Wolfenbüttel, under the employ of Henry Julius, Duke of Brunswick-Lüneburg. He served in the duke's State Orchestra, first as organist and later (from 1604) as Kapellmeister.
His first compositions appeared around 1602/3. Their publication primarily reflects the care for music at the court of Gröningen. The motets of this collection were the first in Germany to make use of the new Italian performance practices; as a result, they established him as a proficient composer.
These "modern" pieces mark the end of his middle creative period. The nine parts of his Musae Sioniae (1605–10) and the 1611 published collections of liturgical music (masses, hymns, magnificats) follow the German Protestant chorale style. With these, at the behest of a circle of orthodox Lutherans, he followed the Duchess Elizabeth, who ruled the duchy in the duke's absence. In place of popular music, Praetorius was now expected to produce religious music.
When the duke died in 1613 and was succeeded by Frederick Ulrich, Praetorius retained his employment. From 1613 he also worked at the court of John George I, Elector of Saxony at Dresden, where he was responsible for festive music. He was exposed to the latest Italian music, including the polychoral works of the Venetian School. His subsequent development of the form of the chorale concerto, particularly the polychoral variety, resulted directly from his familiarity with the music of such Venetians as Giovanni Gabrieli. The solo-voice, polychoral, and instrumental compositions Praetorius prepared for these events mark the high period of his artistic creativity. Until his death, Praetorius stayed at the court in Dresden, where he was declared Kapellmeister von Haus aus and worked with Heinrich Schütz.
Michael Praetorius is said to have died on his 50th birthday, in Wolfenbüttel, Germany and is entombed in a vault beneath the organ of the Marienkirche there.