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It is not clear how this works, but one suspects it involves software-based deep-packet inspection, that can then be used to access the private data.
The software gives its headquarters access to all of the captured accounts.
FinSpy demonstrates how the 'target' can be having a Skype conversation, but allows its headquarters full access to the target's system. This includes the video camera if one is available, any chat messages that are sent and received.
Truecrypt, the popular open-source encryption software, is also used in this video.
The software has keylogger capabilities. This allows the 'agent' to see the password that is being entered to encrypt the files, and file access gives the 'agent' access to the encrypted volume.