After the establishment of the Protectorate, the number of orphanage residents started to rise.
Many incomplete Jewish families, especially refugees from Germany, Austria and the Sudetenland, were unable to provide for their children. After expulsion from all the other schools, some boys came to the Prague orphanage because there still was a Jewish school they could attend. The most famous musical production of the orphanage residents was the Brundibár opera. It was rehearsed at Hagibor and premiered in the orphanage in Belgická street.
In the autumn of 1941 the orphans, teachers and employees of the orphanage started being deported to their death on transports. Out of the 429 who were deported, Kateřina Steinová, author of a book about the Belgická street orphanage, identified 63 who survived until the liberation.