The Second World war cruelly disrupted the transmission of knowledge and tradition in the Protuguese-Jewish community. The library's holdings of books and manuscripts were transported to Germany by the Nazi's, but they were returned in unharmed condition in 1946.

In the period following the Second World war the Ets Haim did not have the financial reserves to provide adequate care for its holdings and the library building. By the 1970's the chronic lack of funding had given rise to a situation whereby the library was such bad condition, that the library was becoming a danger to its priceless collection.

To ensure that the most precious works in the library's holdings would not perish the core collection of the library, consisting of its 500 manuscripts and some 2700 old and rare printings, was given on long-term temporary loan to the Jewish National Library in Jerusalem.