The city has 500 social enterprise businesses - a quarter of the total in Scotland -and the study will look at how these affect health and wellbeing.
It will discover how the organisation affect the health and well-being of people and communities in Glasgow and across Scotland.
The scheme is being run by the Yunus Centre for Social Business and Health at Glasgow Caledonian University (GCU) and will be funded by grants from the Medical Research Council and the Economic and Social Research Council (UK).
Professor Cam Donaldson will act as the project's principal investigator.
He said: "Health inequalities are the unfair and avoidable differences in health across societies. They are compounded by, and related to, continuing high rates of deprivation, unemployment, worklessness and financial exclusion in our poorest communities.
"Many parts of the UK, including Glasgow, suffer disproportionately from such challenges.
"This project is driven by recent thinking about the potential for social enterprise to operate between, and in partnership with, the traditional private and state sectors to address these persistent and widening challenges."
GCU will lead a collaboration between the social enterprise community in Scotland and a number of other universities during the five-year study.
Social enterprises are businesses that direct profit back towards a social mission, rather than distributing it to owners and shareholders.
Glasgow's Impact Arts, which uses art to create social change, is one of these doing good work in the city.
Social enterprises work with the private and public sectors to address social challenges.
But, so far, little is known about the longer-term impacts of social enterprise on health and well-being, despite the organisations' long history in Scotland.
Beginning in January 2014, the project will gather evidence on how social enterprises affect health inequalities.