In 1549, Tomé de Sousa arrived with soldiers, masons, and Jesuits, and planted the capital of Portuguese Brazil on the high cliff above the bay. That choice of geography still defines the city: an upper town of churches and palaces, a lower town of docks and warehouses, and a cliff face between them so steep that by 1873 the city simply ran a steam-powered elevator up it. For more than two centuries Salvador was the seat of Portuguese government in South America. The Dutch took it in 1624 in a surprise assault, and a combined Spanish-Portuguese fleet clawed it back the following year. A second Dutch siege in 1638 failed. In 1672 the cathedral was consecrated, and in 1676 Salvador became the metropolitan see of the colony's archbishopric — the Catholic capital of Portuguese America.

Salvador grew rich on sugar and, later, on the gold that poured down from Minas Gerais. It grew rich, too, on the forced labour of Africans brought in unconscionable numbers across the Atlantic — more enslaved people arrived at the port of Salvador than at any other port in the Americas. The wealth paid for the gilded interior of the São Francisco Church, finished in 1723, and for the Church of the Third Order of Our Lady of the Rosary, begun in 1704 specifically for the city's Black Catholic brotherhood. It also paid, unwillingly, for rebellion. The 1711 Maneta Revolt saw military officers and public officials rise twice against local taxes. In 1835 came the Malê revolt, an uprising organised largely by enslaved Muslim West Africans that terrified the slaveholding establishment of the entire empire. In 1857 the Revolution of the Ganhadores — a strike by African and Afro-Brazilian porters, both enslaved and freed — shut the city's commerce for days.

Brazil's move toward independence passed through Salvador with violence. Portuguese troops held the city under siege from March 1822 until 2 July 1823, the day Bahian forces finally entered and ended Portuguese rule in the province. The date lives on as Dois de Julho, Bahia's most fiercely celebrated holiday. The city grew: 129,000 people in 1872, 174,000 by 1890, 205,000 by 1900. The Lacerda Elevator opened in 1873, stitching upper and lower town together. A Tarde newspaper began publishing in 1912, and the Avenida Sete de Setembro — the city's first grand modernising boulevard — opened in 1916. Salvador was still living inside its colonial bones, but the twentieth century was knocking.

Between 1950 and 1970 Salvador tripled in population, from 275,000 to nearly a million. The old cathedral had been demolished in 1933 to make room for a tram line; new universities, theatres, and stadiums went up; favelas spread across the hills inland. But the deepest change was cultural. In 1949, Sister Dulce — a Franciscan nun from the neighbourhood — began sheltering the city's sickest poor in a converted chicken coop, a charity that became the Obras Sociais Irmã Dulce by 1959 and led to her canonisation as Brazil's first female saint. In 1974, Ilê Aiyê became the first of the great Black carnival blocos, drumming a new pride out of Salvador's African heritage. In 1979, Olodum followed, and within a decade its percussion was crossing the world. The drums of Pelourinho — the cobbled heart of the old city — were now a language recognised from Tokyo to New York.

The 2010 census counted 2.67 million people inside the city itself, with millions more in the surrounding metropolitan area. The historic Pelourinho, restored in fits and starts since the 1990s, is a UNESCO World Heritage Site. Modern Salvador is a tangle of contradictions: poverty and tourism, violence and Candomblé, carnival and Catholicism, Itaipava Arena Fonte Nova holding 50,000 football fans on match day and the Bonfim Church holding millions of pilgrim ribbons tied to its railings. The metro opened in 2014, late, controversial, still incomplete. The city's timeline keeps running. Every year in January, the Lavagem do Bonfim sees women in white wash the church steps with flower water, as they have for more than two hundred years — the deep rhythm under everything else.