McKee was born in Vacaville, California, and spent her formative years in the Seattle area. Taking an early interest in the exposure to music and the theater offered by her father, Bonnie began singing at age five with the Seattle Girls' Choir. She toured Europe in 2000 as a member of its top Prime Voci choir, including a concert in Rome at the request of Pope John Paul II.

Bonnie's youth was somewhat unconventional. She earned the moniker "Trouble" with her participation in the rave scene and difficulties working in traditional schools. Through this period she had a tendency to act beyond her years, using drugs and being unusually open about her sexuality. (Amid rampant speculation, she has stated that she has "no sexual preference.") These experiences raised some eyebrows, and greatly influenced her early songwriting; Blender magazine called her album the written result of being "fifteen, hooked on drugs, dating men twice her age." Eventually she found her way into Seattle'