Joaquím Chissano held a number of prominent posts in Frelimo before his presidency in 1986. In addition to remaining on the Central Committee, Chissano was made secretary of the highly sensitive security department in 1965. He was appointed to both the Political Military Committee and the Executive Committee at the Second Frelimo Congress held in a liberated zone in northern Mozambique in 1968. From there he was assigned as Frelimo's chief representative to Tanzania, a post he held until the end of the war in 1974.
Chissano participated in the peace negotiations that culminated in the Lusaka Agreement of 7 September 1974 and led to full independence from Portugal. After the Lusaka negotiations, Chissano was appointed prime minister in the transitional government by the second Frelimo president, Samora Machel. Chissano was named foreign minister in the first government of the People's Republic of Mozambique formed in June of 1975 and, as such, served in the People's Assembly and in the Council of Ministers. He held the post of foreign minister until 1986.
On 19 October 1986, Samora Machel, president of Frelimo and of the Republic of Mozambique, died along with other prominent Mozambican officials in a plane crash in South Africa. The South African government was implicated in this accident. Subsequently, the Central Committee of Frelimo named Joaquím Chissano president of Frelimo and the People's Assembly confirmed him as president of the republic on 6 November 1986.