She has been awarded three Native American Music Awards, being the first female artist to win "Flutist of the Year," which she won in both 1999 and 2000, as well as winning "Best Female Artist" in 2000. She is also the first Native American woman to have received a Grammy Award for "Best Native American Music Album", and the first Native American person to have won two Grammy's, the first for Beneath the Raven Moon in 2002 and Dance with the Wind in 2006.
In 2007 Mary Youngblood composed and played the flute music on the soundtrack for documentary film, "The Spirit of Sacajawea." 
Ms. Youngblood is on the advisory board of the World Flute Society.
Youngblood has released the following solo albums:
- Sacred Place: A Mary Youngblood Collection 2008, Silver Wave
- Dance with the Wind 2006, Silver Wave
- Feed the Fire 2004, Silver Wave
- Beneath the Raven Moon 2002, Silver Wave
- Heart of the World 1999, Silver Wave
- The Offering (live recording) 1998, Silver Wave
Her work has been included in the following compilations and soundtracks:
- My Mothers Garden by Singer-Songwriter Thea
- Bears with Joanne Shenandoah, Lawrence Laughing, Lyle Lovett, Alice Gomez, and Claude Carmichael
- Prayer for Peace featuring Michel Cusson, and with Mary Youngblood, Joanne Shenandoah
- Many Blessings: A Native American Celebration with Lawrence Laughing, Joanne Shenandoah, Alice Gomez, Robert Mirabal, Tito La Rosa, and Peter Kater
- Sacred Ground: A Tribute to Mother Earth with Robert Mirabal, Star Nayea, Bill Miller, Joanne Shenandoah, Little Wolf Band, and Walela
- Youngblood, Mary. "Musicians Mary Youngblood on Answers.com". Contemporary Musicians. Gale Group. Retrieved 20 March 2013.
- Sonneborn, Liz (2007). A to Z of American Indian Women. New York: Facts of File. ISBN 0816066949.
- Youngblood, Mary. "LOC Holdings". Sound Recording. Library of Congress. Retrieved 20 March 2013.