In the early 1990s, it became clear to co-op leaders that corporate chains were aggressively pursuing the natural foods market nationally, and that these chains had the resources to dominate individual co-ops. Co-op managers in various regions began meeting and forming Cooperative Grocers Associations, with early strategies to provide peer support and to improve operations by collaborating on activities.

By the late 1990s, regional CGAs had gained momentum, and the need for a national coordination of efforts was apparent. Six CGAs, along with advisory support from industry specialists, developed a plan to address this need, and the National Cooperative Grocers Association was born in 1999.

While there were many benefits of the regional membership model, there were also challenges. The NCGA Board retained a consultant to explore different structures to further strengthen food cooperatives, and in 2004 NCGA was reorganized to a single national association with a direct membership model.

NCGA members are cooperative grocery retailers who accept the responsibilities and costs of membership. Membership share requirements to NCGA are based upon annual sales.

NCGA members enjoy many benefits, including participation in the National Cooperative Advantage Program (National CAP), access to marketing and supplier programs, and participation in CoCoFiSt (Common Cooperative Financial Statements, developed and administered by Cooperative Development Services).