Before it was officially founded by Europeans, Zaña was inhabited by the indigenous Moche people. When it was colonized and established by Europeans on 29 November 1563, it was originally named Villa Santiago de Miraflores de Saña.
In its early days, Zaña was a very busy city in Peru, filled with Spanish colonists as well as Indigenous and African slaves. There were also waves of Chinese and Japanese settlers who came looking for work in the sugar plantations. At its peak, Zaña had seven churches and was even considered as an option for the capital of Peru.
Zaña was an extremely important city in the early colonial Americas, and for this reason, it was also targeted by pirates and raids who would ransack the city of its riches. However, the true collapse of Zaña came when in the early 1720s, the Zaña River overflowed flooding the city of Zaña and causing the majority of the European colonists to flee the city, leaving behind their slaves.
Today, much of Zaña’s few inhabitants of descendants of the African and Indigenous slaves of early colonial Zaña. There remains the ruins of many churches and other buildings within the city, and Zaña, besides its small number of residents, is for the most part abandoned. It remains a major archeological site because of its importance in the early colonial Americas and because of its mix of American, European, African, and Asian cultures.