After the March 1944 German occupation, Stern was a member of the German-created Jewish Council (Judenrat, Zsidó tanács) along with Orthodox Community leader Pinchas Freudiger.

Hours after the occupation, Schutzstaffel (SS) officers arrived at Síp utca 12, where PIH was holding its annual general assembly, which abruptly adjourned, when news of the German invasion spread.

[7] The Nazis insisted on the participation of actual community leaders from all denominations, but Stern granted a free hand to naming the specific people to become council members.

[9] Samu Stern wrote in his memoirs in 1946 that "I considered it a cowardly, unmanly and irresponsible behavior, a selfish escape and running away, if I let my fellow believers down now, right now, when leadership is needed the most, when the sacrificial work of experienced and politically connected men could perhaps help them".

[10] Stern and his colleagues were convinced that they could hold together the network of religious communities and aid organizations, and if they do not lead the council, then a some far less competent and influential staff worsens the Jews' chances of survival.

On 19 April 1944, Samu Stern and his colleagues wrote a memorandum to Sztójay, in which they requested an extraordinary investigation and applied for personal audience with the prime minister.

[16][17] The Jewish councils had to function in complete isolation from each other from the very beginning, because the Jews were deprived of all means of communication (e.g. termination of telephone lines, mail censorship and travel ban) soon after the invasion of Hungary.

Regarding the ghettos and atrocities (i.e. deportations) in countryside, the council addressed a series of submissions to the Ministry of the Interior and other departments (including police and gendarmerie), as they were not received in person.

[19] The new regulation also involved personnel changes: Béla Berend, the chief rabbi of Szigetvár, became a member on the recommendation of Zoltán Bosnyák, director of the anti-Semitic Jewish Question Institute.

[23] A council's memorandum with the date 8 June to the Sztójay cabinet urged the suspension of deportations and recommended the Jews' active participation in physical work and labour service.

[28] Sándor Török, the Converted member of the council successfully delivered the collection of eyewitness accounts to Regent Miklós Horthy via the latter's daughter-in-law Ilona Edelsheim-Gyulai on 3 July 1944.

Koszorús blocked the roads with his army and instructed Secretary of State for the Interior László Baky to drive the gendarmes out of Budapest, who were allegedly preparing for a coup d'état against Horthy.

Ferenczy testified the so-called "Baky coup" was a mere fabrication invented by Horthy's staff and the Jewish council together to prevent the deportations in Budapest.

[31] In the upcoming weeks, Miklós Horthy kept promising Edmund Veesenmayer, the Reich plenipotentiary in Hungary, and the collaborationist Ministry of the Interior that the deportations would continue, but he always pushed back the deadlines.

[34] In the second half of September 1944, now under the premiership of Géza Lakatos in a more optimistic situation, the Central Jewish Council attempted to contact the Hungarian Front, an illegal anti-fascist resistance network of banned parties and organizations.

[35] However the Arrow Cross Party took power on 15 October, when Nazi Germany launched the covert Operation Panzerfaust which resulted the arrest of Miklós Horthy.

[37] Therefore, after 28 October, Stöckler acted as de facto chair of the body, but Stern remained the nominal head of the Jewish Council of Budapest.

[36] During the establishment of the Budapest Ghetto in November 1944, its leaders Béla Berend and Miksa Domonkos was in contact with the ailing Stern and Wilhelm, knowing their hiding place, a damp cellar.

[39] To prevent accusations, several former members of all Jewish councils wrote their memoirs, including Samu Stern (with the title Versenyfutás az idővel!, lit.

Szabad Nép, the official newspaper of the Hungarian Communist Party (MKP) connected the amounts to the collaborative behavior of the once Jewish Council of Budapest, who "only helped rich Jews" at that time.