Quaid-e-Azam visited Dhaka, East Bengal, in March 1948. During his speech at the Dhaka University convocation, he declared that 'Urdu and Urdu alone' would be the state language of Pakistan. His intention was to create a symbol of national unity, although this decision later became a point of contention in East Pakistan.

In his address to civil officers in Peshawar in April 1948, Jinnah advised them to perform their duties as 'servants of the people' and to stay away from political pressure. He believed that a neutral, efficient, and honest civil service was essential for the survival and progress of the young nation.

Pakistan faced a severe crisis as India delayed the transfer of the agreed-upon financial and military assets. Jinnah took a firm stance, negotiating through international channels and legal frameworks to ensure Pakistan received its 750 million rupees and its share of military hardware necessary for the defense and administration of the country.

The title 'Quaid-e-Azam' (The Great Leader) was officially recognized and conferred upon Jinnah by the first Constituent Assembly of Pakistan in August 1947. This was done to honor his decades of struggle and leadership that led to the creation of an independent state for the Muslims of the subcontinent.

Quaid-e-Azam appointed his trusted lieutenant and the General Secretary of the Muslim League, Liaquat Ali Khan, as the first Prime Minister of Pakistan. The two worked closely to manage the various crises of the new state, including the division of assets, the Kashmir conflict, and the constitutional deadlock.

The most pressing issue Jinnah faced was the massive influx of millions of refugees migrating from India. He established the 'Quaid-e-Azam’s Relief Fund' and personally supervised the camps in Karachi and Lahore, urging the citizens to show the highest spirit of sacrifice to accommodate their displaced brothers and sisters.

In his historic speech on August 11, 1947, Jinnah explicitly stated that in the state of Pakistan, citizens would find that 'you are free; you are free to go to your temples, you are free to go to your mosques or to any other place of worship.' He envisioned a state where the business of the state would not be concerned with the religion of the individual.

Quaid-e-Azam inaugurated the State Bank of Pakistan on July 1, 1948. This was one of his last major public appearances. In his speech, he emphasized that the bank would symbolize the country's financial sovereignty and tasked it with developing an economic system based on Islamic concepts of social justice and equality.

Quaid-e-Azam served as the Governor General for approximately 13 months, from August 15, 1947, until his death on September 11, 1948. Despite his failing health due to tuberculosis, he dedicated this period to stabilizing the country, rehabilitating refugees, and establishing the foundational institutions of Pakistan.

Karachi was chosen as the first capital of Pakistan because it was a major port city with relatively better infrastructure than other cities at the time. Quaid-e-Azam resided in the Governor General House in Karachi, where he managed the Herculean task of setting up the administrative machinery of the new state from scratch.