As Wiest became established as a film actress through her work in Woody Allen's films, she was less frequently available for stage roles. However, she did appear onstage during the 1990s, in "In the Summer House", "Square One", Cynthia Ozick's "The Shawl", and Naomi Wallace's "One Flea Spare". In 2003, she appeared with Al Pacino and Marisa Tomei in Oscar Wilde's "Salome". In 2005, she starred in Kathleen Tolan's "Memory House". She also starred in a production of Wendy Wasserstein's final play "Third" (directed by Daniel Sullivan) at Lincoln Center.