The app, which launched in early 2017, changes photos with filters to make users look older, younger or swap gender.
But its latest feature was criticised for being racist within minutes of going live.
It allowed people to change their faces to look more black, Asian, Indian or Caucasian in photos.
FaceApp was criticised in April for its "hot" filter which lightened skin tones.
Some users say they were shocked by the new update before even opening the app.
And people who did try out the new feature say they were even more shocked at what the app did to their photos.
Another user suggested that the app's original option of changing your gender is transphobic.
But the app's update and new features, which were published on Wednesday, were quickly pulled by the makers after the backlash.
FaceApp's CEO Yaroslav Goncharov originally promised the features would be removed "in a few hours" and they are no longer available in the app.
"The new filters have been removed," he said in a statement to the press.
"The ethnicity change filters have been designed to be equal in all aspects.
"They don't have any positive or negative connotations associated with them. They are even represented by the same icon.
"In addition to that, the list of those filters is shuffled for every photo, so each user sees them in a different order."