Regional foundations close to the Green Party were set up in the early 1980s. In 1983 there was a first effort to found a national foundation - but it came to nothing. Later in the 1980s three national foundations were established: The feminist Frauenanstiftung, the Buntstift federation of regional foundations, and the Cologne-based Heinrich Böll Foundation. The work of these organisations was later co-ordinated by the umbrella organisation Regenbogen. In 1988 the Green Party recognised Regenbogen as the foundation allied to the party. This meant that from then on the foundation qualified for government funding.

In 1996 a Green Party convention pushed the merger of the separte foundations. The statutes of the new foundation stressed the tenets of gender democracy, and of issues related to migration and diversity. The motion was passed with a large majority. The new foundation took on the name of one of its predecessors - Heinrich Böll Foundation. On 1 July 1997 the new Heinrich Böll Foundation began its operations in its new headquarters in the centre of Berlin.