Amer played a leading role in the military coup that overthrew King Farouk in 1952 and brought General Muhammad Naguib and Colonel Gamal Abdel Nasser to power.

The following year, Amer was promoted straight from major to major-general, bypassing four military ranks, and was made Egypt's Chief of the General Staff.

In March 1964, Amer was made first vice-president to Nasser and deputy supreme commander, with the power to rule for 60 days if the president was incapacitated.

[1] Amer's distinguished career came to a sudden end after Egypt's crushing defeat by Israel in the Six-Day War of June 1967.

[5] This was because Amer's control of the Egyptian military establishment was in line with President Gamal Abdel-Nasser's general policy of making different government institutions fiefdoms to those most loyal to him.

[citation needed] On 6 June 1967 on the second day of the Six-Day War, when Amer heard of the fall of Abu Ageila to Israel, he was said to have panicked and ordered all units in the Sinai to retreat.

In August 1967, Amer, along with over 50 Egyptian military officers and two former ministers, including Shams Badran, were arrested for allegedly plotting a coup to overthrow Gamal Abdel Nasser.