Soutra Aisle was a medieval hospital, a place of refuge for wayfarers and pilgrims, one that welcomed the needy or elderly as well as the sick and infirm. It also acted as a place of sanctuary for fugitives. It stands midway between Edinburgh and the rich Borders abbeys on the Via Regia or Royal Highway, the main Anglo-Scottish road for the medieval period. This spot was originally the place where five roads met, which ensured a regular flow of people in need.

Soutra Aisle was first mentioned in 1164 after King Malcolm IV confirmed the foundation of the charter. The hospital was run by the Augustinian Order, funded by the income from the large hospital estate. Despite being located in a war zone up until 1320, Soutra Aisle continued to grow. It eventually covered an area of 700 square meters, and became one of the three most important hospitals in Scotland at the time.

Soutra Aisle was of both national and international importance up until the 1460s, when it experienced a rapid decline. Soutra Aisle lost its lands, which caused an almost instant loss of funds that was devastating to the hospital. The estate was confiscated and handed to the Trinity College Hospital in Edinburgh because the Master of the Hospital, Stephen Fleming was accused of misconduct.

It only survived because it became the burial vault of the Pringle family. This new purpose saved the church from the same fate as the rest of the site, which saw its stone carted away and repurposed in nearby building projects.

Archaeological excavations have turned up rare seeds, sourced from all over the world, that were used for their medicinal properties, including opium poppies, cloves, and hemlock.