The project was promoted by the Botín Foundation, a private endowment foundation created in 1964 by Marcelino Botín Sanz de Sautuola and his wife, María del Carmen Yllera Camino.

The building, consisting of two volumes of different sizes supported on columns and partially suspended over the sea, was designed by the Italian architect Renzo Piano, winner of the Pritzker Prize in 1998, and is organised into two volumes linked by a structure of spaces and walkways in the form of a main distributor. The western volume is dedicated to art, with a 2,500 square metre exhibition hall; a shopping and restaurant area is located in its glazed ground floor. The smaller east volume is for educational activities, with a large terrace overlooking the bay of Santander and a 950 square metre covered plaza on the ground floor.

Light and lightness, two of the essential aspects of its conception, stand out in it. The light is reflected in its ceramic façade, made up of 280,000 discoidal pieces that adapt to the geometry of the building. The construction is supported by pillars and columns, forming a cantilever over the bay of Santander and the old Albareda and Maura docks, while respecting the height of the treetops of the Jardines de Pereda.

The project also affected the Pereda Gardens adjacent to the building, whose surface area increased from two to four hectares, mainly due to the undergrounding of road traffic.

According to Emilio Botín, former president of the Botín Foundation, the installation cost 77 million euros. Other sources put the final cost at 100 million euros. In 2013 the Foundation had committed an annual budget of 12.5 million euros for the maintenance and development of activities at the Centre.

The renovation of the Pereda gardens was inaugurated to the public in the summer of 2014, while the opening of the centre took place on 23 June 2017, three years late.