The ELCA merger of 1988 brought together nearly 30 Lutheran colleges and universities previously governed by the ALC and LCA under a variety of arrangements. When the new denomination was formed each college was asked to choose one of three groups to approve their trustees; the National Church Convention, a regional Synod convention, or an Association of Congregations convention. Gustavus of course chose the latter option, and in 1989 the Association of Congregations was formed.
Currently there are over 500 members of the Association, the largest of its kind in the ELCA. The Association of Congregations elects the board of trustees at its annual convention in April, and its congregations serve as the college's primary connection to the church.
In 2002, Gustavus Adolphus College was awarded an automated DNA sequencer and related software from LI-COR® Biosciences, valued at nearly $70,000. Gustavus was chosen from a pool of 30 applicants at undergraduate institutions in the nation to receive this equipment.