The project began with an attempt to restore puffins to Eastern Egg Rock Island in Muscongus Bay, about 6 miles (9.7 km) away from Pemaquid Point.
After spending their first 2–3 years at sea, it was hoped they would return to establish a new colony at Eastern Egg Rock rather than Great Island.
To lure them ashore and encourage the birds to explore their home, wooden puffin decoys were positioned atop large boulders.
The Center features a live video display of puffins and other seabirds from Seal Island National Wildlife Refuge.
Exhibits also include natural history displays, the seabird conservation work done by the Audubon Society and its partners, and a film about Project Puffin.