War began in January 1963 with military support from Cuba, China, and the Soviet Union. PAIGC liberation sympathizers and recruits among the rural population thrived and in a relatively short time, the PAIGC succeeded in reducing Portuguese military and administrative control of the country to a relatively small area of Guinea. Guineans in the 'liberated territories' ceased unlawful mortgage payments to Portuguese landowners as well as payment of taxes to the Portuguese Colonial administration.
The PAIGC seized the branch stores of the Companhia União Fabril (CUF), Mario Lima Whanon, and Manuel Pinto Brandão companies in the areas they controlled, banne the use of Portuguese currency and established a Marxist administrative and governmental bureaucracy, which organized agricultural production, educated farmworkers on protecting crops from destruction from government attacks, and opened collective Armazéns do Povo (people's stores) to supply urgently needed tools and supplies in exchange for agricultural produce. By 1967 the PAIGC had carried out 147 attacks on Portuguese barracks and army encampments, effectively controlling 2/3 of Guinea.
In 1968, The next year, Portugal began a new campaign against the PAIGC with the arrival of the new Portuguese Governor, General António de Spínola. Spínola instituted a series of civil and military reforms, intended to first contain, then roll back the PAIGC’s control of much of rural Guinea. He started a 'hearts and minds' propaganda campaign designed to win the trust of the indigenous population, tried to eliminate some of the discriminatory practices against native Guineans, began a massive construction campaign for public works including new schools, hospitals, improved telecommunications and road networks, and a large increase in recruitment of native Guineans into the Portuguese armed forces serving in Guinea as part of his Africanization propaganda strategy. Between 1968-1972, Portuguese forces increased their offensive posture, in the form of raids into PAIGC-controlled territory. The Portuguese also attacked the political structure of the nationalist movement, which culminated in the assassination of Amílcar Cabral, a founder of the PAIGC, in January 1973. Nonetheless, the PAIGC continued to increase its strength, and began to heavily press Portuguese army.
By 1969 PAIGC forces were increasingly supplied with modern Soviet weapons and equipment; SA-7 rocket launchers, radar-controlled AA cannon, and several Ilyushin Il-14 bombers which, undermined Portuguese air superiority, preventing the destruction of PAIGC encampments from the air.
By 1970 the PAIGC had officers learning to fly MIGs and to operate Soviet-supplied amphibious assault crafts and APCs in the Soviet Union. In retaliation, the Portuguese Air Force (FAP) began to use Napalm and defoliants to deny PAIGC Freedom fighters the cover and concealment needed for ambushes and to hinder assistance from the neighboring Republic of Guinea, Portugal commenced Operação Mar Verde or Operation Green Sea on 22 November 1970 in an attempt to overthrow Ahmed Sékou Touré, the leader of the Republic of Guinea and staunch PAIGC ally. The attempted coup d’état failed, but the war escalated as Algeria and Nigeria began offering the PAIGC support.
The United Nations passed several resolutions condemning all Portuguese cross-border attacks in Guinea, through United Nations Security Council Resolution 290 and United Nations Security Council Resolution 295.
On 25th April, 1974 the Carnation Revolution, a left-wing military led revolution, broke out in Portugal ending the authoritarian dictatorship of Estado Novo. The new regime quickly ordered cease-fire and began negotiating with leaders of the PAIGC. On 26th August 1974, after a series of diplomatic meetings, Portugal and the PAIGC signed an accord in Algiers, Algeria in which Portugal agreed to remove all troops by the end of October and to officially recognize the Republic of Guinea-Bissau PAIGC controlled government.
Portugal recognized the full independence of Guinea-Bissau on 10th September, 1974, after eleven-and-a-half years of armed conflict. With the coming of independence, the PAIGC moved swiftly to extend its control throughout the country. They had already unilaterally proclaimed the country's independence a year before in the village of Madina do Boé, an event that had been recognized by many socialist and non-aligned member states of the United Nations. A one-party state controlled by the PAIGC and headed by Luís Cabral, half-brother of Amílcar Cabral was established and given the choice of either returning home with their families, belongings, and full payment until the end of December that year, or joining the PAIGC military, a total of 7,447 African soldiers serving in Portuguese native commando units, security forces, and armed militia chose not to join the PAIGC ruling party. The PAIGC executed them after Portuguese forces ceased hostilities.