It was conceived as an open shelter for religious works related to the church site; transparent glass panels were soon added.

[1][2] The creation of the museum was one of the first initiatives of the government organization now known as National Institute of Historic and Artistic Heritage, known at the time as SPHAN.

SPHAN was created in 1937 and in the same year the architect Lúcio Costa (1902–1998) was sent by the organization to Rio Grande do Sul to analyze the remnants of the Sete Povos das Missões (Seven Peoples of the Missions) and propose conservation measures for the site.

[1][2] The architect, Lucas Mayerhofer, directed the stabilization works in the (Church of São Miguel) and designed a museum building to house statuary related to the site.

The museum became part of the UNESCO World Heritage Site titled "Jesuit Missions of the Guaranis" in 1984.