Collection operation is one of museums' essential tasks – something that the nature of the collections, their size and history defines. Aboa Vetus Ars Nova museum is the home of two considerable collections; Matti Koivurinta Foundation's art collection and the collection of archaeological finds from the museum area's soil. The finds are owned by Aboa Vetus Ars Nova but some finds from the museum area are in the collections of the Museum Centre of Turku. Whereas the collection of archaeological finds gets larger by every excavation, the art collection is expanded by purchases and donations.

Research is also strongly attached to collection operation; the goal is always to study collections and discuss new themes that e.g. fresh archaeological finds might bring up. The museum's own collections are an essential part of the exhibitions where the aim lies in a thorough background research and careful and interesting, visitor-considerate, presentation.

In addition to the art collection and the collection of archaeological finds, the museum also has a photograph collection, archives and a reference library into which both museum literature and reports as well as studies to do with Aboa Vetus Ars Nova are added.