Wheldrakes in York, Espresso Yourself in Scarborough and Betty's in Harrogate have all been named in the list based on TripAdvisor reviews from retailer Coffee Friend.
The York coffee shop was fifth and Scarborough's shop in 11th, both of which are rated five out of five on the site, and Betty's in 20th which is rated as four and a half out of five.
The research has looked at the highest rated coffee shops across the UK with more than 100 reviews based on TripAdvisor reviews - taking excellent, terrible and overall ratings into account.
Of the 627 reviews on TripAdvisor, Wheldrakes received almost 550 'excellent' marks and just three reviews said it was 'terrible'.
For Espresso Yourself, it has no 'terrible' marks and 133 'excellent' reviews out of 157.
But the figures will have been skewed somewhat for the popular Betty's, which had more than 7,000 reviews, over 4,000 'excellent' marks and 139 'terrible' ratings.
Aurimas Vainauskas, CEO of Coffee Friend, said: “The UK is now a nation of coffee lovers and with the country returning to more normal times, we’re helping the people of Britain find the best cafes in the best places.
“Our research has looked at the highest rated cafes across the country and found some of the better known, and lesser known, joints to grab a favourite drink and a bite to eat.”
Top of the list was the Big Moose Coffee Company in Cardiff, which had 295 reviews, three ratings of 'terrible' but 287 marks of 'excellent'.