He served as prime minister of the puppet government of the German-occupied Protectorate of Bohemia and Moravia from 27 April 1939 to 27 September 1941 but maintained contact with the government-in-exile.

[1] After the Austrian declaration of war on Serbia, Eliáš was called up for service with the Austro-Hungarian Army and was sent with the Prague 28th Infantry Regiment to Galicia.

[1] They were volunteer armed forces fighting on the side of the Entente Powers during World War I (France, Britain, Italy, Russia) with the goal of winning the Allies' support for independence and were ultimately successful.

Eliáš was later dispatched to France, where he studied at the officer school at St Maixent, and was later assigned to the 21st Czechoslovak Regiment as a platoon commander.

Its replacement was discussed at the end of April 1939, with President Emil Hácha thinking Alois Eliáš would be a good choice for prime minister because the popularity that he had acquired during his earlier military career would legitimise the puppet regime.

[citation needed] On 25 March 1939, Adolf Hitler in a speech to all of the various state secretaries held at the Reich Ministry of the Interior stated that Jews should be "excluded" from the public life of the protectorate, but that this was "not the direct responsibility of the Reich" as the "Jewish question" in the protectorate would "develop on its own accord" with no involvement from the Germans.

[2] Upon being appointed premier by President Hácha on 27 April 1939, Eliáš was ordered to "intensely" prepare a set of anti-Semitic laws for the protectorate.

[6] The Israeli historian Livia Rothkirchen wrote that Eliáš was an active Free Mason known for his Czech nationalism, and there is no evidence that he personally ascribed to anti-Semitism.

[6] Eliáš submitted to Neurath a list of 1, 000 Czech Jews who had made notable contributions to public life, and asked the Reichsprotektor to give them exemptions from the anti-Semitic laws.

[3] The same day, Eliáš sent a message to Beneš declaring his loyalty to the government-in-exile and asked for his a priori consent "in such opportunistic political moves" on his part which would help with "evading national or economic disaster.

[3] After the invasion of the Soviet Union, code name Operation Barbarossa, was launched on 22 June 1941, there was an increase in resistance in the protectorate, mostly in the form of sabotage of weapons meant for the Wehrmacht.

[3] Eliáš started to meet in public in various parks and cemeteries with Milan Reiman, a courier for the Central Committee of the illegal Communist Party of Czechoslovakia.

With the help of his urologist, Miloš Klika, sandwiches were laced with botulism toxin, tuberculosis-causing Mycobacterium tuberculosis, and typhus-causing Rickettsia bacteria.

[14] Přibáň and Hvíždala wrote that in the Czech memory of World War Two, the defining episode was the Lidice massacre of June 1942 while the story of Eliáš tends by contrast to be neglected.

[14] Přibáň and Hvíždala maintained that Eliáš showed extraordinary courage and managed to lessen at least some of the burden of the occupation, but that his story is neglected because while "...the Czech nation has heroes, but it is not so fond of them because it prefers victims".