Family-owned Colpi, which can trace its roots to before the start of the first World War, made its initial delivery to the American owned chain earlier this month.
Colpi currently operates out of retail premises in Milngavie, where it has been since 1928, and Clydebank.
The business, which employs up to 25 people during the summer months, still makes its ice-cream in a traditional way from unpasteurised milk delivered from a dairy farm in West Dunbartonshire.
No additives, chemicals or E numbers are added to the ice-cream, which is also gluten free.
The Whole Foods tie-up came following a meet-the-buyer event organised by industry body Scotland Food & Drink in April.
A shortlist of businesses were then asked to meet executives from America who came to Scotland to look at potential new products. They liked the ice-cream and the supply deal was set up.
Terri Colpi, the company's business development director, said: "It is a good move for us and I am quite optimistic about how it will go.
"We have the manufacturing capacity to supply Whole Foods as we can do this at both Milngavie and Clydebank."
Ms Colpi said the warm weather so far this summer had helped early sales at Whole Foods.
Colpi is also sold through some Peckham's outlets in Glasgow and in some convenience stores around the west of Scotland, although it has no plans to pursue any supermarket deals at the moment.
The Colpi family originally established the business with shops in Gourock and the Whiteinch area of Glasgow before moving to the Milngavie premises 85 years ago.
The Clydebank site was added in 1990.
The company is now run by Ms Colpi and her brother Martin and the duo have spent the past two years modernising the brand and processes, while retaining the "artisan" production methods.
Ms Colpi, who commutes from Hampshire to take up her role in the business, said: "We will always retain our method of making ice-cream as it is what sets us apart.
"We have two options for expansion and that is through wholesale or opening more retail outlets in other locations.
"It is the wholesale route that we are going to do at the moment."
Whole Foods started out in Austin, Texas, in 1978, specialising in organic food. It now has more than 300 outlets, with annual revenues in excess of £5 billion. The company opened its Giffnock store in November 2011 in what was its first UK site outside of London.
In Scotland it employs about 140 people and stocks hundreds of Scottish-made products from honey and chocolate to salmon and oysters.
Although not all stock is organic, every product has to pass stringent Whole Foods tests.
Those include making sure the item is produced without the use of pesticides, herbicides, hormones, antibiotics, artificial colourings or flavourings, hydrogenated fats or MSG.
Ms Colpi said: "Whole Foods rightly wanted to scrutinise what we do and make sure we complied with their standards.
"After lots of phone calls and online filings, they were satisfied, but the whole process has been impressively professional, and perfectly friendly."
Comedian Kevin Bridges and television presenter Jenni Falconer are shown on the Colpi Facebook page enjoying ice-creams in the cafes.