Following first publication in 1996, the staff continued to work on The Site of Big Shoulders, adding new content and recruiting new contributors and staff members. In 1998, the magazine took another step forward by getting its own Web hosting environment and Internet domain name: sobs.org. The staff pulled together a new "city-on-its-side" design concept and relaunched version 2.0 with a new look and more content.

Interest in The Site of Big Shoulders continued to grow – both through increased submissions and burgeoning Web site traffic – and around 2000, it became clear that the informal, kitchen-table nature of The Site of Big Shoulders needed to change. As put by Chief Operations Officer Jake Eldridge: "We need to either grow it, or kill it." The Site of Big Shoulders staff decided on the former and began to formalize operations and pursue official not-for-profit status, as the magazine had always been non-commercial in nature.

One first step toward not-for-profit incorporation was applying for and receiving a Community Arts Assistance Program (CAAP) grant from the City of Chicago, which provided the initial funding needed for filing state and federal 501(c)(3) not-for-profit incorporation documents. The Site of Big Shoulders received its probationary 501(c)(3) status in 2002 and its final 501(c)(3) status in 2007. Two succeeding CAAP grants provided funding for promotional materials and development help.

The Site of Big Shoulders also underwent another design and technology overhaul during this time, retaining the city-on-its-side design, but refining it and re-coding all of the index pages to better support contemporary Web browser technologies. Around this time The Site of Big Shoulders began employing Web applications for both publishing purposes and to support production activities.