The origins of the Pottery Museum date back to the 1940s, when the Barcelos City Council began works on the Paço dos Condes de Barcelos, removing an existing street and installing an underground room there. In the early 1950s, the ethnographer Joaquim Sellés Paes made a donation to the Barcelos City Council, consisting of more than 700 ceramic items and artifacts related to their production, from various Portuguese pottery centres, especially from Barcelos, which would become the first group of pieces in the museum's collection.

On 4th May 1963, the Regional Museum of Ceramics was inaugurated during the Festas das Cruzes, nearly 15 years after Sellés Paes’ donation. In the following year, Eugénio Lapa Carneiro, a professor of Technical Education at the Industrial and Commercial School of Barcelos, was appointed by the City Council to take over the museum’s direction. A few years later, the name of the institution was changed to the Museum of Popular Portuguese Ceramics, reflecting a broader geographical scope of its collection. Until the 1980s, the museum operated in the small room installed beneath the Paço dos Condes de Barcelos, with limited facilities for an ever-growing collection, resulting from fieldwork and donations.

At the beginning of the 1980s, the Barcelos City Council decided that the museum needed a new space, abandoning the room that had long been insufficient to fulfil its museological objectives. Thus, in 1982, the process of relocating to the Casa dos Mendanhas Benevides Cyrne was initiated, a building that had previously housed the old Industrial and Commercial School of Barcelos, beginning with works to renovate and adapt its various areas. At the same time, the museum’s name was changed once again, and it would now be called the Pottery Museum. Upon completion of the works and the transfer of the collection to the new premises, the museum opened its doors to the public on 29th July 1995.

As the new millennium approached, the Pottery Museum became part of the Portuguese Museum Network, and in 2007, it established the Education and Animation Service. Near the end of the 2010s, new museological demands and the need to engage with new audiences led to the development of a new intervention project to adapt and expand the building. After works of renovation, enhancement, and expansion, the museum reopened to the public on 31st August 2013, now offering a larger exhibition area for its permanent exhibition. In the following years, the Municipality of Barcelos co-founded the Portuguese Association of Ceramic Cities and Towns (AptCVC) in 2018, with the Pottery Museum being the main link between the entities. A year later, it became a member of the International Academy of Ceramics, one of the most prestigious global institutions in the field.

Between 2020 and 2022, during the COVID-19 pandemic, the museum's operations were significantly restricted due to the sanitary measures in place. Once this turbulent period had passed, the museum inaugurated the permanent exhibition "Olaria de Portugal" on 6th May 2023, celebrating the institution’s 60th anniversary. Its importance and prestige led to the museum receiving the Ceramic Medal in 2024 from the AptCVC, in recognition of its more than 60 years of service to culture and heritage.

Throughout its history, the Pottery Museum has significantly expanded its collection, growing from the initial 700 items to 7,000 in just three decades, and today it holds around 11,000 pieces. The museum has been pivotal in the preservation, study, and promotion of Portuguese ceramics, particularly that of the Barcelos pottery centre.