Johannes married Eva Katharina Ruffra on 15 Jan 1781 in Bergzabern, Pfalz. Eva was born on 19 Jan 1753 in Oberotterbach, Pfalz; died on 25 Mar 1806 in Oberotterbach, Pfalz. [Group Sheet] [Family Chart]

1. Johannes Joseph Schäffer was born on 17 Sep 1785 in Oberotterbach, Pfalz; died on 7 Feb 1847 in Oberotterbach, Pfalz, Bayern.
2. Maria Dorothea Franziska Schäffer was born in 1788 in Pfalz; died on 26 Jan 1850 in Oberotterbach, Pfalz, Bayern.

Johannes married Catharina Ittensohn on 3 Aug 1806 in Oberotterbach, Pfalz, Bayern. Catharina was born on 31 Dec 1768 in Oberotterbach, Pfalz, Bayern; died on 20 Jan 1814 in Oberotterbach, Pfalz, Bayern. [Group Sheet] [Family Chart]

Johannes married Margaretha Kastner on 14 Jul 1814 in Oberotterbach, Pfalz, Bayern. Margaretha was born in 1767 in Oberotterbach, Pfalz, Bayern. [Group Sheet] [Family Chart]