Gaining commission as a Second lieutenant in the British Indian Army, Khan served with distinction in the Burma and North African campaigns as part of the Allied effort in World War II.

Khan retired shortly after the 1965 war and embarked on a career in national politics, after which he was appointed to serve as the Governor of West Pakistan, a position he held from 1966 to 1969.

The first batch of IMA, known as "The Pioneers", also produced India's first Field Marshal Sam Manekshaw, and Smith Dun, the future commander-in-chief of the Burmese Army.

[3] He participated well in the World War II on the side of the United Kingdom and served well in the Burma Campaign and North African theatre as part of the Norfolk Regiment of the British Indian Army.

[3] In 1942, his heroic action for valor won him the praise and was appointed as Member of the Order of the British Empire (MBE) for "gallant and distinguished services in the Middle East.

[3][9] In 1952, his last field assignment included his role as General Officer Commanding (GOC) of 8th Infantry Division positioned in Quetta before stationed at the GHQ.

[18] After reviewing the aerial view of the area and getting directions from President Ayub to make way for Maj General Yahya Khan, General Musa controversially relieved GOC Major-General Akhtar Hussain Malik and handed over the command of the 12th Division to Major-General Yahya Khan, which resulted in critical time delays of troops movements and eventual failure of the operation.

[20] His strategy based on classical trench method supported by armory, artillery and airpower was tactically powerful and successful as it stopped the advancing Indian Army but politically unsuccessful due to the country being party of the peace treaty brokered by the USSR in 1965.

At the time of his retirement in 1966, General Musa was a famed and popular military figure which led President Ayub Khan to appoint him as the Governor of West Pakistan.

[24] In 1967, he became Governor of West Pakistan until submitting his resignation on 2 March 1969 when General Yahya Khan imposed martial law to takeover the presidency.

[26] After the general elections held in 1988, Governor Musa controversially dissolved the provincial assembly on the then-Chief Minister Zafarullah Khan Jamali's advice.

[3] In his honour, the provincial Balochistan government established a vocational school, the General Muhammad Musa Inter-College (GMMIC), in Quetta, Pakistan in 1987.