In 1800, he married Helene Marie Zoege von Manteuffel (1774–1842); from a noble Baltic-German family with roots in the 14th century. They had three children together. His first son, Wilhelm, was born in Saint Petersburg in 1802, and also grew up to become a painter. The other children were Gerhard (1806–1884), and Adelheid (1808–1874).
In 1820, he was killed by a thief while on his way into Dresden from his studio in the suburb of Loschwitz. He is buried in the Old Catholic Cemetery, Dresden.
The asteroid 11313 Kügelgen is named after him and his son Wilhelm.[1]