Hammerschmidt left Freiberg in 1633, through his mentor Stephan Otto, taking a post as organist for Count Rudolf von Bünau in Weesenstein, but returned to Freiberg the next year as an organist. He was married shortly after his return there, and of his six children three died in infancy. In 1639 he left Freiberg again, moving to Zittau, where he succeeded Christoph Schreiber as organist; he remained in Zittau at this post for the rest of his life. While musical life in Zittau was severely damaged by the Thirty Years' War, including the decimation of the choirs and general reduction in musical standards, Hammerschmidt survived; after the end of the war in 1648 musical life slowly regained its former high standard.