During the Third Reich the congregation and the umbrella, to which it belonged, fell into deep disunity (For the general outline see Evangelical Church of the old-Prussian Union and Struggle of the Churches).
The polarisation within the old-Prussian Church started already before the Nazi takeover in 1933.
In the orderly election of the presbyters and synodals on 13 November 1932 the Nazi Faith Movement of German Christians ran for the first time for seats in the presbyteries of the congregations and synods of the old-Prussian church body.
The Positive Union, a conservative Kirchenpartei with traditions back in the 19th century, had no candidates running for presbytership in the congregation of Jerusalem Church, thus many nationalist parishioners rather voted for the German Christians.
Among the congregations in the inner city of Berlin that of Jerusalem Church was one of the four, where the German Christians gained already at this time a, narrow though, majority of the seats in the presbytery (German: Gemeindekirchenrat).

 Jerusalem Church then belonged to the deanery (German: Kirchenkreis) Friedrichswerder I, whose superintendent (cleric in chief in a deanery) Friedrich Geest (1868–1940), pastor of confidence of Paul von Hindenburg, held an ambiguous position as to the Nazi opposing Confessing Church.
The liberal D. Alfred Fischer (1874–1940), since 1901 pastor at Jerusalem Church and opposing the German Christians, and his younger colleague Dr. Rudolf Köhler (until May 1933) had hard times with them dominating the presbytery since 1932.

At the unconstitutional premature re-election of the presbyters and synodals, discretionarily decreed by Hitler for 23 July 1933 the German Christians could increase their share of the seats in the presbytery to 65%.
Their presbyterial speaker Walter Hartig, president (Obermeister) of Berlin's professional association of the men's tailors (Herrenschneiderinnung), tried to establish the Führerprinzip within the congregation.
Fischer, being by his office as senior pastor chief executive of the presbytery, was supported in his fight by the other opposing presbyters Justizrat Eschenbach, Köhler, Otto Nagler, the director Seibt, and the merchant Zaepke, but Fischer, being already an old man, did not stand the permanent quarrels.

Following the merger with the congregation of the New Church one of its pastors, Dr. Curt Horn, started to also serve at Jerusalem Church and Horn joined in May 1934 the German Christians.
Thus in 1934 Eschenbach, a longtime presbyter, resigned from the presbytery.
Fischer retired from ministry in 1936.

Soon the German Christians in the presbytery fell out with each other, some siding with Hartig (now representing the radical Thuringian branch of the German Christians), others with Horn, blaming each other to use psychological terror and authoritarianism against each other.
Horn, preserving some dignity as a pastor, requested the presbytery to reaccept Martha Fränkel (then living in Kochstraße 62), a parishioner of Jewish descent.
Geest sided with the somewhat more moderate Horn, but in 1940 the consistory of the March of Brandenburg ecclesiastical province within the old-Prussian Church decided to completely dissolve the presbytery of the united congregation of Jerusalem Church and New Church, for it had turned – with all its quarrels – incapacitated to function.

After 1936 Fischer still held contact with some parishioners.
Christiane Ilisch (daughter of the Protestant literary historian Dr. Heinrich Spiero, classified a Jew, meaning within the Nazi ideology a member of a genetic group not a religion, which one could choose or secede from) and her husband asked Fischer to baptise their children.
The German Christian-dominated presbytery denied it to them, regarding Christianity a religion reserved for persons of so-called Aryan blood and therefore to be denied to persons fully or partially of Jewish descent.
Fischer thus baptised the children in a ceremony held in the Ilischs' private apartment.
In 1941 Jerusalem Church, whose services after all the quarrels hardly
During the Third Reich the congregation and the umbrella, to which it belonged, fell into deep disunity (For the general outline see Evangelical Church of the old-Prussian Union and Struggle of the Churches). The polarisation within the old-Prussian Church started already before the Nazi takeover in 1933. In the orderly election of the presbyters and synodals on 13 November 1932 the Nazi Faith Movement of German Christians ran for the first time for seats in the presbyteries of the congregations and synods of the old-Prussian church body. The Positive Union, a conservative Kirchenpartei with traditions back in the 19th century, had no candidates running for presbytership in the congregation of Jerusalem Church, thus many nationalist parishioners rather voted for the German Christians. Among the congregations in the inner city of Berlin that of Jerusalem Church was one of the four, where the German Christians gained already at this time a, narrow though, majority of the seats in the presbytery (German: Gemeindekirchenrat).
 Jerusalem Church then belonged to the deanery (German: Kirchenkreis) Friedrichswerder I, whose superintendent (cleric in chief in a deanery) Friedrich Geest (1868–1940), pastor of confidence of Paul von Hindenburg, held an ambiguous position as to the Nazi opposing Confessing Church. The liberal D. Alfred Fischer (1874–1940), since 1901 pastor at Jerusalem Church and opposing the German Christians, and his younger colleague Dr. Rudolf Köhler (until May 1933) had hard times with them dominating the presbytery since 1932.
At the unconstitutional premature re-election of the presbyters and synodals, discretionarily decreed by Hitler for 23 July 1933 the German Christians could increase their share of the seats in the presbytery to 65%. Their presbyterial speaker Walter Hartig, president (Obermeister) of Berlin's professional association of the men's tailors (Herrenschneiderinnung), tried to establish the Führerprinzip within the congregation. Fischer, being by his office as senior pastor chief executive of the presbytery, was supported in his fight by the other opposing presbyters Justizrat Eschenbach, Köhler, Otto Nagler, the director Seibt, and the merchant Zaepke, but Fischer, being already an old man, did not stand the permanent quarrels.
Following the merger with the congregation of the New Church one of its pastors, Dr. Curt Horn, started to also serve at Jerusalem Church and Horn joined in May 1934 the German Christians. Thus in 1934 Eschenbach, a longtime presbyter, resigned from the presbytery. Fischer retired from ministry in 1936.
Soon the German Christians in the presbytery fell out with each other, some siding with Hartig (now representing the radical Thuringian branch of the German Christians), others with Horn, blaming each other to use psychological terror and authoritarianism against each other. Horn, preserving some dignity as a pastor, requested the presbytery to reaccept Martha Fränkel (then living in Kochstraße 62), a parishioner of Jewish descent. Geest sided with the somewhat more moderate Horn, but in 1940 the consistory of the March of Brandenburg ecclesiastical province within the old-Prussian Church decided to completely dissolve the presbytery of the united congregation of Jerusalem Church and New Church, for it had turned – with all its quarrels – incapacitated to function.
After 1936 Fischer still held contact with some parishioners. Christiane Ilisch (daughter of the Protestant literary historian Dr. Heinrich Spiero, classified a Jew, meaning within the Nazi ideology a member of a genetic group not a religion, which one could choose or secede from) and her husband asked Fischer to baptise their children. The German Christian-dominated presbytery denied it to them, regarding Christianity a religion reserved for persons of so-called Aryan blood and therefore to be denied to persons fully or partially of Jewish descent. Fischer thus baptised the children in a ceremony held in the Ilischs' private apartment. In 1941 Jerusalem Church, whose services after all the quarrels hardly 
Jerusalem Church (Berlin)