She starred in the terrorist thriller The Siege (1998), reportedly earning her $3 million, and as a woman who develops a psychic link with a serial killer (played by Robert Downey Jr.) in the dark psychological thriller, In Dreams (1999). Also in 1999, she turned in a great performance as a materialistic suburban real estate agent in the darkly funny hit film, American Beauty, earning an Academy Award nomination for Best Actress. In 2000, she starred in What Planet Are You From? as a woman who marries an extraterrestrial invader, played by Garry Shandling.

Bening and Beatty have four children: Kathlyn Elizabeth, Ben, Isabel Ira Ashley, and Ella Corinne. .