An initial excavation revealed an arched corridor almost 6ft high, and uncovered pottery fragments and gaming pieces, a complete chamber pot, and other artefacts.
Archaeology professor Steven Driscoll, part of the Glasgow team, said the site was uniquely well preserved.
“What’s unusual is that it hasn’t been messed with. This is a loo that hasn’t been flushed for 500 years. We have a kind of sealed environment, containing artefacts like the earliest known piece of Scottish music, which we found scratched into pieces of slate,” he said.