Muungano wa Wanavijiji is the primary organization—a social movement of residents of informal settlements and markets. As of early 2017, it is constituted by 935 slum-based community groups, spread across urban centers in 21 of the Kenya's 47 counties. This includes the cities of Nairobi, Mombasa, Kisumu and Nakuru.

These community groups, which share methodology and federate to form Muungano, are individually autonomous. Typically, they seek formal registration, either as self help groups or community based organizations. When they intend to carry out a slum-upgrading project or when they require to present as a community, they graduate into cooperative societies or neighbourhood associations.

Muungano groups, within close proximity of each other, form local networks. These networks enable peer learning between the groups, and are a first line of support for the individual groups. The networks also federate at the city level. These city networks are a platform to engage city authorities and advocate on issues of common interest.

The Muungano movement draws representation from the city networks to form a national movement leadership. This national leadership provides the strategic thrust and decision making for the entire alliance.

The Muungano movement itself is not registered as an organization—for contracting purposes it relies on its two support organizations:

Akiba Mashinani Trust (AMT) is a capital fund which develops financing strategies and products, and raises capital for slum improvement projects. It also holds assets such as land and investments for communities, up until the communities are sufficiently organized to hold and manage these themselves. While AMT has a professional secretariat of 10 staff, the majority in its board of trustees are drawn from Muungano – this is because AMT holds funds and assets on behalf of slum communities in Muungano.

SDI Kenya provides professional, planning, social, data, and technical support to Muungano wa Wanavijiji. It consists of around 7–10 professional staff. SDI Kenya was established in late 2014, and is a company limited by public guarantee.