Being the senior most Muslim Civil Servant in the Indian Ministry of Defence, Iskander Mirza was appointed as the first defense secretary of Pakistan at the time of Independence. He served in the same position for about seven years. With the dismissal of the United Front’s ministry in East Pakistan, Governor General Ghulam Muhammad decided to enforce Governor’s rule in the province and appointed Iskander Mirza as Governor in May 1954. Assuming charge of the province, he openly declared that he would not hesitate to use force in order to establish peace in the province. The first step he took as Governor was to order the arrest of 319 persons, including the two most outspoken leaders, Mujib al Rahman and Yusuf Ali Choudhury. By mid June, the number of persons arrested had reached 1051, including 33 assembly members and two Dhaka University Professors. By doing so he might have been able to bring immediate peace but had sown a permanent seed of hatred for the Central government in the hearts of people of East Pakistan. From October 1954 to August 1955, Iskander Mirza served as the Interior Minister, and then as the Minister of States and Frontier Regions in the cabinet of Prime Minister, Muhammad Ali Bogra. Ghulam Muhammad, due to his illness, went on two months leave and thus Iskander Mirza assumed the duties of acting Governor General on August 7, 1955. However, this acting charge was made permanent in the times to come. He appointed Chaudhry Muhammad Ali, another bureaucrat, as the Prime Minister of the country. When the Constitution of 1956 was adopted, the title of the head of the state of Pakistan was changed from Governor General to President but the duties and powers of the office did not change to a great extent. The Constituent assembly unanimously elected Iskander Mirza as the first President of Pakistan.

Primarily, Iskander Mirza was a Civil Servant and it is widely believed that he lacked parliamentary spirit. He was of the view that because of the lack of training in the field of democracy and low literacy rate among the masses, democratic institutions can not flourish in Pakistan. He never had a very high opinion about Pakistani politicians and once referred to them as ‘mostly crooks and scalawags’. He wanted controlled democracy for Pakistan with more powers for the civil bureaucracy. He believed that the Magistrate should be given the same powers, which he used to enjoy during the British Raj. He thought that politicians should be given the power to make policy but they should not interfere in administration. Iskander Mirza was also a great advocate of the One Unit scheme. In his opinion religion was to be be kept at a distance from politics.

History documents that like his predecessor, Ghulam Muhammad, Iskander Mirza was also a power hungry person and wanted to dominate the political scene of the country by hook or by crook. Being the head of the state, he always remained active in power politics and played the role of a king-maker. He proved to be an expert in palace intrigues. He took full advantage of the weakness of the politicians and played them against each other. To offset the influence of the Muslim League, he played an active role in the creation of Republican Party. During his short span of four years as the head of the state, four Prime Ministers were changed. Most historians believe that Iskander Minza was the one mainly responsible for this political un-stability.

Iskander Mirza felt threatened from the reorganization of Muslim League and the alliance of Awami League with the Punjabi groups in mid 1958. On October 7, he issued a proclamation abrogating the 1956 constitution. According to the proclamation, the central and the provincial assemblies were dissolved and the first Marshal law was enforced in the country. Iskander Mirza himself remained President and appointed Ayub Khan as the Martial Law Administrator and supreme commander of the armed forces. Ayub Khan proved to be smarter than the politicians and refused to act as puppet in the hands of the President. On October 27, Ayub Khan compelled Iskander Mirza to leave the country, assumed the title of President himself and announced that martial law would continue in order to give legal cover to certain reforms he wanted to put through.