[2] In 1626 he returned to Cremona, and in 1627 became maestro di cappella at the cathedral there, but he only remained for four years, moving to Bergamo to accept a similar position in 1631.

In 1646 he went back to Cremona for the final time, serving as maestro di cappella at the Laudi della Madonna until his death in 1665.

In sacred music Merula followed the lead of Monteverdi, and often used the techniques of the elder composer; however he also did some new things, such as writing motets for solo voice accompanied by strings.

Merula's secular music includes solo madrigals with instrumental accompaniment, sometimes using the Monteverdian stile concitato tremolo effect, and in formal design prefiguring the later Baroque cantata with its division into aria and recitative.

He also wrote canzonettas, dialogues, keyboard toccatas and capriccios, a Sonata cromatica, and numerous other pieces which display an interest in just about every contemporary musical trend in north Italy.