(from ingame System -> Help)
The Bestiary will keep track of how many monsters you have defeated, conveniently listing off all of the loot that they are capable of dropping along with the drop chances. It will also show you how many you have captured as well, enabling you to begin harvesting those possible loot drops every 2-3 hours.
This harvesting is manual, but there is a Loot All button provided in the top left of the Bestiary window to make this process simpler. Additionally, the Epic Shop upgrade has also been made available that will auto-collect Bestiary harvests as soon as they are ready, providing a permanent passive income of potentially rare items.