On 3 February, 1956 , Awami League leaders, during a meeting with the Chief Minister, demanded that the subject of provincial autonomy be included in the draft constitution. On 14 July, the Awami League at a meeting adopted a resolution opposing the representation of the military in the administration. The resolution was moved by Bangobondhu. On 4 September an anti-famine procession was brought out under the leadership of Bangobondhu defying Section 144. At least three persons were killed when police opened fire on the procession in Chawkbazar area. On 16 September, Bangobondhu jointed the coalition government, assuming he charge of Industries, Commerce, Labor, Anti-Corruption and Village Aid Ministry.

Pakistan's President, Major General Iskandar Mirza, and the chief of Pakistan's army Genera Ayub Khan, imposed martial law on 7 October, 1958 and banned politics. Bangobondhu was arrested on 11 October. Thereafter, he was continuously harassed through one false case after another. Released from prison after 14 months, he was arrested again at the jail gate. After his release from prison, Mujib started organising an underground political body called the Swadhin Bangal Biplobi Parishad (Free Bangla Revolutionary Council), comprising student leaders in order to oppose the regime of Ayub Khan and to work for increased political power for Bengalis and the independence of East Pakistan. He was briefly arrested again in 1962 for organising protests.

Following Suhrawardy's death in 1963, Mujib came to head the Awami League, which became one of the largest political parties in Pakistan. The party had dropped the word "Muslim" from its name in a shift towards secularism and a broader appeal to non-Muslim communities. Mujib was one of the key leaders to rally opposition to President Ayub Khan's Basic Democracies plan, the imposition of martial law and the one-unit scheme, which centralized power and merged the provinces. Working with other political parties, he supported opposition candidate Fatima Jinnah against Ayub Khan in the 1964 election. Mujib was arrested two weeks before the election, charged with sedition and jailed for a year. In these years, there was rising discontent in East Pakistan over the atrocities committed by the military against Bengalis and the neglect of the issues and needs of East Pakistan by the ruling regime. Despite forming a majority of the population, the Bengalis were poorly represented in Pakistan's civil services, police and military. There were also conflicts between the allocation of revenues and taxation. Unrest over continuing denial of democracy spread across Pakistan and Mujib intensified his opposition to the disbandment of provinces.