The convent's church still bears some evidence of its initial period, but has been subjected to several changes between the 17th and the 19th centuries; especially in regard to its contents. The church of the Ordem Terceira, built between 1745 and 1747 was filled, during the following decades, with altarpieces, pulpits and valances in rococo design. Later, in the beginning of the 19th century the stalls and pipe organ, both in neoclassic fashion, were added. 

The museum was established in the 20th century, during the 70ies, to be exact, through the creation of the Instituto Limiano - Museu dos Terceiros. In 2002 the town hall and this institute signed an agreement towards the restoration and joint management of the museum. It reopened to the public in 2008, it is a reference in religious art in all northern region.