In New York, Spektor gained a firm grounding in classical music from her piano teacher, Sonia Vargas, a professor at the Manhattan School of Music. Spektor studied with Vargas—whom Spektor's father had met through violinist Samuel Marder, Vargas's husband—until she was 17. Although the family had been unable to bring their piano with them from Russia, Spektor found a piano on which to practice in the basement of her synagogue, also utilizing tabletops and other hard surfaces for this purpose.
Although she had always made up songs around the house, Spektor first became interested in songwriting during a visit to Israel with the Nesiya Institute in her teenage years. Attracting attention from the other children on the trip for the songs she made up while hiking, she realized she had an aptitude for songwriting. Following this trip, she was first exposed to the work of Joni Mitchell, Ani DiFranco, and other singer-songwriters, which gave her the idea that she could create her own songs. She began writing her first a cappella songs around age 16, and wrote her first songs for voice and piano when she was nearly 18.
Spektor completed the four-year studio composition program of the Conservatory of Music at Purchase College in Purchase, New York within three years, graduating with honors in 2001. Around this time, she also worked briefly at a butterfly farm in Luck, Wisconsin, and studied in Tottenham, England for one semester.