A decade later, however, Holy Trinity then became overcrowded as more German immigrants arrived in Dubuque. Congregants formed an organization to build a new church in 1863. They bought a piece of land from a local estate in 1864 and construction began that year. After three years, the church was dedicated on February 10, 1867.
By the late 2000s, the St. Mary's was experiencing financial difficulties and church membership had been in decline. This prompted church officials in 2009 to recommended selling the building. The final mass was held on May 10, 2010. For several years afterward, the church sat vacant. In 2014, local residents and members of the business community established the Friends of St. Mary's organization with the purpose of developing ideas for the former church site. In 2016, they finished this work and announced the creation of Steeple Square.