Margarita has worked as a prosecutor since 1990. In 1995-2004, she was the head of the Sofia District Prosecutor’s Office.

In 2004, she was removed by the former Chief Prosecutor, Nikola Filchev, and went on to become a professor at the National Justice Institute teaching young prosecutors.

In September 2006, the new Chief Prosecutor, Boris Velchev, appointed Popova his spokesperson. She holds the status of a member of the Sofia District Prosecutor’s Office delegated to the Supreme Prosecutor’s Office of Cassation.

Since 2006, Popova has also served the head of the special unit for investigating frauds with EU funds at the Supreme Prosecutor’s Office of Cassation.