In 1686, Kirch went to Leipzig. There, he observed the great comet of 1686, together with Christoph Arnold. At Leipzig, Kirch also met his second wife, Maria Margarethe Winckelmann (1670-1720), who had learned astronomy from Arnold. In 1688, he invented and charted the now obsolete constellation Sceptrum Brandenburgicum, the Brandenburg Scepter. Later, in 1699, he observed comet 55P/Tempel-Tuttle but this observation was not recognized until later analysis by Joachim Schubart.
Kirch studied the double star Mizar, and discovered both the Wild Duck Cluster (Messier 11) (1681) and Globular Cluster M5 (May 5, 1702). He also discovered the variability of the Mira variable Chi Cygni in 1686.
He died at Berlin at the age of seventy-one.
Kirch was married to the self-taught astronomer Maria Winkelmann.