Jacob Stolterfoht was married three times. On 2 October 1626 he married Dorothea Kirchmann, daughter of the Lübeck polymath-philologist . She died on 18 June 1637, by which time the marriage had yielded seven recorded children. Three further recorded children resulted from Stolterfoht's second marriage, which took place on 25 June 1638 and was to Anna Hackhusen. His third marriage, on 3 August 1664, was to Gertrud Steinmann who the following year also predeceased him. Jacob Stolterfoht is known to have died in Lübeck on 4 March 1668. His portrait, by , bore his epitaph and survived in the Marienkirche till 1942.