During and after the war
According to plans of the NSDAP, the Synagogue was to be demolished "at costs of the Jewish capital", the cantor’s house was to be renovated and assigned to the party. This scheme was, however, not realised. The SA-Standarte 21 moved into the cantor’s house and applied for the flat of the non-Jewish couple Diete.
The stay of the couple was rejected by the SA as they had "formerly managed the affairs of the Jewish temple and of the Rabbi and it was unbearable that a former janitor at a Jewish temple continued tasks at the SA."
The IKG was required to repair the building’s "structural damage" at its own costs. As the Religious Community was not in a position to do so, the municipality of St. Pölten, which had "aryanised" all the real estate of the IKG, bought the Synagogue. The money was stored on a frozen account of the "Central Office for Jewish Emigration", a "branch" of the Sicherheitsdienst. The IKG could not freely dispose of this money.
In 1942, the Synagogue was used by the Arbeitsamt (Labour office) as a reception camp for Russian forced labourers. A part of the building was adapted for this reason by the municipal Bauhof and equipped with 76 paillasses. In 1945 the building was further damaged by bomb splinters. The Red Army used the Synagogue as granary and furniture store and returned it to the municipality in April 1947. The restoration to the IKG Vienna as legal successor dragged on until June 1954.
The IKG Vienna requested the municipality St. Pölten to return the rental revenue; the municipality St. Pölten in turn requested the compensation for the maintenance costs and for the purchase price. After an offset of all expenses, the IKG Vienna paid 24.252,98 Austrian Schilling to the Municipality of St. Pölten for the restoration of "aryanised" property.
In the following years, the unused building decayed further, hundreds of pigeons nested in the cupola which was in danger of collapsing. In 1975, the IKG asked to buy the Synagogue from the municipality of St. Pölten. The Niederösterreichischen Nachrichten (NÖN, Lower Austrian Newspaper) published a report which stated the following under the title of "Jewish temple for sale" and "do you need a Jewish temple": "The offer of the Israelite Religious Community causes St. Pölten’s city fathers considerable headache. The Israelite Religious Community offered the Jewish temple for sale and the municipality will probable accept; however, there is some uncertainty what to do with the building. – ›Don’t you have any potential buyers for it‹ the NÖN was asked by the mayor Mr Schickelgruber; and the municipal councillor Mr Gruber is convinced that the building can for the time being be maintained with a minimum of clean-up operations. [...] The wishes of the Israelite Religious Community included a commemorative plaque as well as the care for and maintenance of the Jewish cemetery by the municipality. The temple could, however, also be dismantled and the area could be offered to the health insurance which has already declined, though. ›For a new building the location is disadvantageously located, for a parking lot it is too small.‹ Who is in need of a Jewish temple?" – If nothing else, the author of this not marked article could at least be accused of a lack of sensibility.