Zapata denies the allegations and faces up to 25 years in prison, according to the Colombian newspaper El Tiempo.
At least some of her daughters were under the age of 14 when they were first forced to have sex.
The Colombian city of Medellín has experienced a rebirth in the last decade, moving away from its image as the violent home of infamous drug lord Pablo Escobar and rebranding itself as a safe tourist destination and a business-friendly hub in the new Colombia.
Street gangs control neighborhoods and young women are sold into a life of prostitution.
Old habits, however, die hard.