At the end of his tenure, he was appointed for, and served as, the Governor and Commander-in-Chief of the Armed Forces of the Portuguese Guinea from 1968, and again in 1972, during the period of the Overseas War, where his administration favoured a policy of respect for ethnic Guineans and the traditional authorities.

At the same time, he continued to practice a range of initiatives in the War, from clandestine meetings (he met secretly with the President of Senegal, Léopold Sédar Senghor, at one point) to armed incursions to neighbouring states (such as Operation Green Sea, which saw the assault by Portuguese Army Commandos into Conakry, Guinea).

In November 1973, he returned to Lisbon, on the invitation of Salazar's successor, Marcello Caetano, to head the Overseas portfolio: which he refused, due to the government's intransigence on the Portuguese colonies.

A month later, on 17 January 1974, he was asked to be the Vice-Chief of the Defence Council of the Armed Forces, on the advice of Francisco da Costa Gomes, a post that he would be removed from in March.

On 25 April 1974, as a general in the MFA (Movimento das Forças Armadas or Armed Forces Movement), he received from the President of the Council of Ministers, Marcello Caetano, the rendition of the Government, which was in refuge in the Carmo Barracks.

Spínola met with Mobutu Sese Seko, the President of Zaire, Hilgard Muller, South African Foreign Minister, and Hugo Biermann, South African Defence Chief, on 15 September 1974, on Sal Island in the Portuguese Cape Verde, crafting a plan to empower Holden Roberto of the National Liberation Front of Angola, Jonas Savimbi of UNITA, and Daniel Chipenda leader of the MPLA's eastern faction (a rival of MPLA leader Agostinho Neto) while retaining the façade of national unity; Mobutu, the South Africans, and Spínola wanted to diminish Neto's importance and present Chipenda as the MPLA leader (Mobutu particularly preferring Chipenda to Neto because Chipenda supported autonomy for the province of Cabinda, an Angolan exclave surrounded by Zaire and the Republic of the Congo, and Neto did not).

[4] His appeals to the maioria silenciosa (″silent majority″), to resist the political radicalization of the left after the failed coup of 28 September 1974, and his tentative involvement in the rightist counter-revolution on 11 March 1975 (wherein he fled to Brazil)[5] were examples that Spínola had changed his allegiances.