At the age of 14 in keeping with the family tradition and like his elder brother Friedrich, he also began his military career with the Tyrolean Kaiserjäger Regiment and was commissioned as a Leutnant on 27 October 1877.

In 1882, Eugen took an examination before a commission assembled by Archduke Albrecht that verified his suitability to attend the military academy at Wiener Neustadt.

Eugen became then the sole archduke to attend the several year long course at the academy (1883–1885) and subsequently successfully graduated as a fully trained general staff officer.

When in 1909 the possibility of a war against Serbia was in the air he alongside Archduke Franz Ferdinand and General Albori was named as a presumptive army commander.

When Archduke Wilhelm suddenly died, Eugen was enthroned as the new Hoch- und Deutschmeister on 19 November 1894 and in this office he also proved himself very effective.

Finally he was transferred in December 1914 to replace Oskar Potiorek and assume the post of commander of the forces in the Balkans (Balkanstreitkräfte) with his headquarters at Peterwardein.

Together with his chief of Staff, Feldmarschall-Leutnant Alfred Krauss, a very talented military theoretician with a decisive and vigorous character, he reorganized the hard hit 5th Army.

From March 1916, it functioned as Heeresgruppen-Kommando Erzherzog Eugen in Tyrol to the exclusion of the remaining parts of the front and at the beginning of the execution of the 12th battle of the Isonzo as Heeresfront Erzherzog Eugen with the allied German 14th Army and Heeresgruppe von Boroević under command but Heeresgruppe von Conrad was not immediately subordinate.

In the further course of the war Eugen had to transfer more and more of his troops to the hard fighting Isonzo Army so that he soon had to manage without reserves in his own theatre of operations.

Against the will of the chief of the general staff, Generaloberst Baron Arz von Straußenburg, the Emperor Karl released Eugen from active service on 18 December 1917.

After Russia's withdrawal from the war and the shortening of various other fronts (Isonzo, Carinthia, Dolomites), the senior generals pushed at the Piave.

The last foreign minister Graf Andrassy and the member of parliament Dr. Franz Dinghofer of the German nationalist party had discussed this.

Additionally he was the possessor of a host of foreign awards and decorations: Following the collapse of the monarchy Eugen first settled in Lucerne and then at Basel where he lived modestly in a hotel from 1918 to 1934.

He participated at monarchical rallies, attended veterans' meetings and placed himself again at the service of the dynasty even though he himself no longer believed that he would live to see the restoration.

Eugen received, probably with the intervention of Hermann Göring and other senior military figures, a rented house at Hietzing where he survived the Second World War.