Climate change is one of the major factors behind the puffin population drop on the Isle of May.
Experts say the rising water temperature is forcing the birds' main food source north and that has impacted numbers.
The Isle of May sits five miles off the Fife coast, playing host to the third-largest puffin colony in the UK and acting as a barometer for what is happening with the species across the British Isles.
There are more than 40,000 pairs of puffins there and they return from winters in the North Atlantic or North Sea every year to the island to pair bond for life and raise their young.
However, researchers who carry out a census every five years found the issue of climate change is having a huge impact on the numbers.
A huge drop of 33% was recorded between 2008 and 2013, but there has been destabilisation in recent times.
Puffins have begun to adapt their eating habits by consuming more sprats, a larger fish than sand eels, which can sustain their young for longer.
David Steel, Isle of May reserve manager, said: "What we are finding is that numbers actually plummeted between 2008 and 2013.
"We lost nearly 33% of our puffins just on this island. I'm glad to say things have stabilised since then, so some good news, but we've got to see the recovery complete."
Researchers are calling on the public to take photos of the puffins in order to help with records that will assist with compiling population numbers.
Mr Steel said a number of issues contributed to the decline in bird numbers, but that climate change was "without a doubt the biggest concern".
"If we talk about a change in sea temperature of just one degree, the plankton move north," he said.
"The sand eels follow then, and then the predators - such as the puffins - which feed on them, they don't have their food source.
"That's what the problem is - it all has a big knock-on effect.
"Puffins can live up to 30, 35 years. They can tolerate one poor season. But when it's year after year after year of poor summers, that's when the population can be affected and things can go bad."