In 1501, Italian navigator Américo Vespúcio organized an expedition of reconnaissance and discovered a large bay; he named it the All Saint's Bay, because it was November 1st, All Saint's Day. Still, the foundation of Salvador only happened in 1549, when Tomé de Souza came to Brazil with the objective of building a capital city for this Portuguese colony. The location had already some prestige at that time, because it had become a trade center (warehouse) between the West and the East.

In 1550, the capital city started developing. This happened thanks to the arrival of the first slaves from Angola, Benin, Congo, Ethiopia, Mozambique, Nigeria and Senegal. The black men's work generated economic growth, improving the port activities, sugar and tobacco production, as well as cattle raising in the Reconcavo region. Later, the international trade and the exports of sugar produced in the surroundings of All Saint's Bay would transform Salvador into the most important city of the southern hemisphere in the XVII and XVIII centuries.

In 1553, Tomé de Sousa returned to Lisbon and was succeeded by hidalgo Duarte da Costa, who governed until 1558, when Mem de Sá (1558-1572) was appointed to his place. With the latter, the general government was finally consolidated.

Being considered prosperous, the city was invaded several times. One of the largest invasions was from the Dutch, lasting from May 1624 until April 1625. The Dutch were interested in Brazilian sugar, which contributed to their finances, and their economy was being threatened at the time by an embargo from Spain, who ruled Brazil at the time.

Salvador was seat of the Brazilian government until 1763, when it was transferred to Rio de Janeiro. The dissatisfaction with the transference of the capital city from Salvador to Rio de Janeiro and the growth of social problems and misery generated a lot of anti-colonial manifestations in Salvador from 1794 to 1798, among them the "Conjuração dos Alfaiates", "Inconfidência Baiana", "Conspiração dos Búzios", "First Brazilian Social Revolution" and also "Sedição dos Mulatos", which occurred under the influence of the illuminist Philosophy and the French Revolution.

In the first half of the XIX century, the Portuguese Royal Family persecuted by Napoleon Bonaparte, Emperor of France, landed in Salvador. During his stay in the Brazilian capital city, Prince Regent D. João opened Brazilian ports to the ships of so-called friendly nations and founded a School of Medicine and Surgery, the country's first medical faculty and a great center of studies and humanistic culture, which had a wide influence on Brazilian medical sciences during the XIX century.

Political movements for the independence of Brazil were growing all over the colony and Salvador always took a decisive part in those movements. However, Bahia remained occupied by Portuguese troops even after the independence was proclaimed near the Ipiranga River in 1822. After months of battle and the Portuguese capitulation, the National Army took the city on July 2nd 1823, consolidating the Brazilian Independence. This date started being celebrated by the Bahia's people as Bahia's Independence Day, besides being a motive of national pride, because it marked the people's fight for freedom.

In 1835, Salvador staged the most important manifestation of resistance against slavery that happened in Bahia - the "Revolta dos Malês" ("Malê's Rebellion"). The "malês" (term used to represent the group of African Muslims) fought against the slavery and the imposition of Catholicism.

In 1837, a military rebellion took place, known as "Sabinada". The "sabinos" proclaimed Bahia "fully and permanently cut out from the so-called central government from Rio de Janeiro, and considered a free and independent State". The "Sabinada", defeated by Federal troops, was the last armed revolution to occur in Bahia.

Other conflicts took place in Salvador in the XX century, such as the military bombing in 1912 and the famous popular protest called "quebra-bondes" (street riot which resulted in damaged streetcars) occurred during the 1930s Revolution against the high prices of streetcar fares.

From the 1960s onwards, the city started a renovation process. Salvador started modernizing after the construction of Bahia's Administrative Center, which transferred the public administration from the center of city, and the restoration of Pelourinho, which granted it the title of Humanity Patrimony as the largest colonial architectural complex in Latin America.