The findings have been published by Reviva Coffee, the premium, sustainability brand owned by Gulf Oil International Ltd.
Coming in a close second is Edinburgh, where 85% of its 560 coffee shops are not part of a chain.
In third place is Bristol. Known for its vibrant identity, brimming with creativity and colour, where coffee-lovers can choose from 347 independent coffee shops, 86.3% of all those in the city.
Fourth place goes to Brighton and Hove, with 329 outlets, of which a whopping 90% are independent. Fifth is Sheffield, with 314 coffee shops, of which 85% are rated as independent.
If you are wondering how London managed to miss out on a top five spot, then the team at Reviva say the capital of England was removed from consideration because there was no data available for the entire area.
A spokesman said: “With there being an endless demand for coffee, over the years we have seen an incredible rise of every type of coffee shop from corporate chains to independently-owned.
“The independent coffee shop market has grown by 4% in the last financial year and we decided to investigate which UK city is the best for independent coffee shops.