After his studies he initially worked as a high school teacher in Pärnu but from 1909 to 1922 was pastor in Laiuse.

During the interwar period Kõpp was also leader of the Christian People's Party.

Among other things, land owned by the church was confiscated and the printing of religious books banned.

In 1944, when the Red Army re-occupied Estonia and drove out the Germans, Johan Kõpp fled to Sweden.

Half of the active priests in Estonia at the time made the same decision to flee.