Glasgow-based Grameen in the UK will use the money to boost the availability and affordability of business loans in deprived communities.
Grameen provides micro-credit loans of up to £1,000 to help disadvantaged people start or develop a small business.
The investment was secured through the SIS-managed Social Growth Fund.
It provides loans to social enterprises and the third sector.
Grameen aims to alleviate economic, health and social inequalities in some of Scotland's poorest communities.
The initiative is facilitated by Glasgow Caledonian University (GCU) and inspired by the Grameen system in Bangladesh, which was created by GCU Chancellor and Nobel Peace Prize winner Prof Muhammad Yunus.
Grameen has so far distributed more than £600,000 through 450 loans to small businesses across Glasgow which were not served by mainstream financial services.
Grameen chief executive Kevin Cadman said the investment from SIS was a "significant milestone" for his organisation.
He added: "Ultimately our aim is grow our services across Scotland and then the UK, and we now have a strategy in place, backed by investment, which will enable us to start planning for the future."
SIS chief executive Alastair Davis said: "In the aftermath of the Brexit vote, we are finding that many social enterprises and charities are taking a cautious approach to growth, partly due to a misconception around the availability of finance.
"Before postponing any investment decisions, we'd encourage any organisations with a lending requirement to come and speak to us about taking on investment.
"Grameen in the UK is a great example of how SIS can help to provide the capital required to increase positive social impacts."
A micro-finance provider is to scale up its operations after securing £250,000 from Social Investment Scotland (SIS).