Jens-Martin Rauen began developing the first version of ChurchTools in 2004 to organize the contact database of his own youth group in Elim Hamburg. The system was soon used to organize the contacts of the entire congregation.

In the following years, other congregations who heard about the system also asked to use it, and by 2010 several dozen congregations in Germany, Austria, Switzerland and France had ChurchTools as their internal system. Jens-Martin Rauen continued to develop the system and expanded its functionalities according to the needs of the churches.