Customers and staff at The Sands café on North Beach were taken aback by the arrival of the adult seabird.
Café assistant Lynn Horman said customers had tried to return the puffin to the beach, but it came back.
She said: "He looked a bit bedraggled, but didn't seem afraid – in fact, he initially sat next to a cocker spaniel and they both appeared quite happy."
Staff at The Sands called RSPB Bempton Cliffs and volunteer Allan Dawson went to collect the bird from the café.
He said: "Fortunately, the puffin looked healthy and wasn't injured.
"Sometimes seabirds become waterlogged because their preening glands don't work correctly.
"It seems this was the case with the puffin. So apart from being tired, he was in fine fettle."
The puffin will be cared for by Jim Ward, of Yorkshire Coast Wildlife Rescue, until he is strong enough to be returned to the wild.
