An English-Prussian bishopric was founded in Jerusalem in the year 1841. This alliance was the basis for the Protestants to settle in Jerusalem. Samuel Gobat, the second protestant bishop, purchased a compound on the Mount of Zion for the burials of relatives of both churches in the bishopric in the year 1848. In the year 1886 this alliance resigned because of the political general conditions. But it was decided to pursue the Cemetery together. For this purpose a committee of cemetery was founded 1906 which consisted an equal number of seats taken by the English and by the Germans. This committee owns still the administration of the Cemetery.
In the year 1917 a field for war graves for the German and Austrian soldiers which had been fallen in this area since 1916 was constructed. It was called the “nicht-konfessionelle Insel auf dem Prostestantenfriedhof” (“a non-confessional island on the protestant cemetery”).
After the Israeli war of Independence and the foundation of the state (1948–1967) the Cemetery was no longer useable for the churches which lay in the eastern part of Jerusalem, because the Cemetery laid directly west of the armed truce line between Israel and Jordan.
The Mount of Zion Cemetery is until today the one and only burial place of the German speaking protestant congregation in Jerusalem. Because of the everlasting right of ease in the Middle East the Cemetery possesses only a few unoccupied graves which are reserved for the resident Protestants.