Arthur's estate has bestowed the huge sum to the Ali Forney Center in New York, which helps home young members of the lesbian, gay, bisexual and transgender (LGBT) communities who have been disowned by their families.
Bosses at the charity have confirmed the money will go towards a new 12-person property, which is to be named in Arthur's honour.
Ali Forney Center Executive Director Carl Siciliano says, "We work with hundreds of young people who are rejected by their families because of who they are.
"We are overwhelmed with gratitude that Bea saw that LGBT youth deserve as much love and support as any other young person, and that she placed so much value in the work we do to protect them, and to help them rebuild their lives."
Arthur lost her battle with cancer in April (09). She was 86.