Gordailua was designed by architects Pedro Astigarraga and José Leon Lasarte and erected between 2009 and 2011. The slats on the four sides of the rectangular building give it the appearance of a container. Its unusual outline stands out among the surrounding homes and industrial buildings. The centre occupies a site of just under one acre (3,445 square metres), including the adjoining gardens. The three-storey building itself has a total floor area of 9,116 square metres (98,000 square feet).
The items are held in eight stores, covering 70% of the total floor area (around 6,000 square metres or 65,000 sq ft.). In the depositories, the objects are kept at appropriate levels of humidity and temperature, depending on their composition. In all cases, the relative humidity is kept below 60% and the temperature between 18 and 20º. There are also special rooms conditioned for metals, paper and fabrics.
In addition, Gordailua has offices, restoration workshops (for archaeological, palaeontological, ethnographic and artistic objects), registration and photography rooms, quarantine and transit zones, a library, two consultation and research rooms and two multi-purpose rooms, which are used for seminars, lectures, exhibitions, etc.
A geothermal device and photovoltaic roof panels help reduce the building's energy dependency. In the event of a power failure, an autonomous generator comes into service to maintain climate conditions.