In 1993, Bhalla worked as a summer intern with John Kornblum in the New York City Public Health Laboratories.[2] In 1995, she graduated magna cum laude with a Bachelor of Arts from Columbia College (New York).[2] One summer during her undergraduate studies, Bhalla researched in Teri Melese's lab at Columbia University where she learned of her interest in cell biology.[2] Bhalla completed a Doctor of Philosophy at University of California, San Francisco in 2002.[2] She completed her doctoral research in Andrew W. Murray's lab where she researched mitotic chromosome segregation in yeast.