The beginnings of a German seamen‘s mission date back to the 19th century and are based on the ideas and convictions of Johann Hinrich Wichern, that Church should spend more time taking care of the seamen‘s needs than done so far.

On 14 December 1895, members of the Centralausschuss für die Innere Mission [Central Committee for the Inner Mission] of the German Protestant Church founded the Deutsche Evangelische Seemannsmission Berlin, the so-called "Berlin Committee", a precursor of the current foundation.

In 1932 the organisation was registered as an association under the name of Deutsche Evangelische Seemannsmission (Mitteldeutscher Zweig) e.V. [German Protestant Support of Seafarers' Dignity (Central German area)], one of the founding members being Pastor Martin Niemöller. After World War II, the Mitteldeutscher Zweig in turn was one of the founding members of the worldwide network of the Deutsche Seemannsmission in Bremen.

As a consequence of the division of Germany, the association was no longer able to maintain its former facilities in various city ports from the 1950s onwards. They were included in the network of the Deutsche Seemannsmission e.V. in Bremen. Being the only seamen‘s mission in the area of the Protestant church in Berlin, Brandenburg, and in Upper Lusatia, the association still remained committed to supporting the seamen's welfare.

After the end of communism in 1989, the Deutsche Evangelische Seemannsmission (Mitteldeutscher Zweig) e.V. established first contacts with Estonia. From the 1990s onwards, in cooperation with other countries it laid the groundwork for setting up Estonian seamen‘s missions.

Per amendment of the charter in 2007, the addition "Mitteldeutscher Zweig" was omitted. The Deutsche Evangelische Seemannsmission e. V. (DESM), Berlin, had existed as an association until summer 2017 and was then transferred into a foundation that pursues the same objectives. Also for the future, the Stiftung Seemannshilfe - Deutsche Evangelische Seemannsmission has made it its priority to be actively involved on a voluntary basis to help seamen in the ports of the Baltic Sea.