Running Adobe Media Encoder on a system with a virus scanner, AME might not delete its cache/work files. Those files can be several gigabytes of size.

To delete those cache files go to:

[users folder]\[your profile]\AppData\Roaming\Adobe\Common

There you’ll find a folder “Media Cache Files”, delete everything inside. Make sure AME is closed when you do so. In some cases you also need to disable the virus scanner first.