Benedek was attacked on the right flank by the entire army of King Victor Emmanuel II of Piedmont-Sardinia, just a few kilometers north of Solferino in the Battle of San Martino.

After the Austrian defeat, Benedek was appointed Chief of the General Quartermaster Staff on 31 January 1860, and to the governorship of Hungary in April.

On 20 October 1860 Benedek assumed command of the Austrian forces in Lombardy-Venetia, Carinthia, Carniola, the Tyrol and the Adriatic Coastland and was awarded the Grand Cross of the Order of Leopold with War Decoration on 14 January 1862.

Benedek was a staunch believer in the concept that the army was the chief guardian of the Habsburg monarchy and needed to protect it from liberal and nationalist forces; loyalty to the dynasty and monarch were paramount and suspicion of the civilian professional and business classes followed.

In a circular to his officers in March 1861 he warned against "international revolutionaries, lawyers and doctors without practices, ambitious and money-hungry journalists, dissatisfied professors and schoolteachers" as well as "debt-ridden nobles and cowardly magnates" who threatened the monarchy.

[2] A year later he further stated in Verona that the army's purpose was "to serve, fight, and if necessary die with honor for the emperor and supreme warlord.

"[2] Benedek believed in a traditional concept of war where valor and courage were of chief importance, where "simple rules" were superior to "complicated calculations".

[5] While the Prussians advanced against and defeated Austria's German allies (Hanover, Hesse-Kassel, and Saxony), Benedek remained in a defensive posture.

Urged by Emperor Franz Joseph's emissary, Lieutenant Colonel Friedrich Beck, to advance, Benedek and his staff replied the army was still not ready.

Concerning himself with issues of military dress and ceremony and emphasizing the importance of close combat in the coming battles (despite the superiority of the Prussians' needle guns), Benedek only deployed his troops at the end of June.

[6] When the Prussians crossed into Bohemia, Benedek failed to mass his forces against the separate enemy formations and suffered defeats across his front (except for a costly stand at Trautenau).

However, the Prussians had achieved their objectives and were suffering a cholera outbreak while the Austrians were desperate for an end to the fight; an armistice was signed on 21 July.