As well as the supermarket, which will be called Grounded Organics, there will be two certified commercial kitchens - one to make their Frillys branded gluten free food and the other to make organic foods, to be sold at the supermarket.
Mr Tomkies said the big difference is they will be producing a lot of their product, rather than buying and selling it.
A common, costly problem for organic supermarkets is wastage, he said, but they will minimise this by using "spotty" produce to make products.
"We are aiming to make 99 per cent of it on site," said Mr Barnes.
They said the products will also be sold online to cater to the growing online shopping market.
The cafe, with its gluten-free menu, will move to the supermarket's South Wairarapa location, which is under wraps at the moment.
Mr Barnes, who was diagnosed with Coeliac disease five years ago, started up in 2011 with his wife Kate and began supplying Frillys food to other cafes and restaurants around the country.
When he was diagnosed, he said he had to find another way to keep working in the trade he loves and spent a year and a half developing recipes. "When you've been cooking for 17 years, you can't just walk away."
The idea for the supermarket came about when the lease for the cafe came up for renewal.
Mr Tomkies and Mr Barnes met when Mr Barnes' dog, which was rehomed, ended up with the Tomkies.
Over a coffee, Mr Barnes said the lease was up for renewal and Mr Tomkies saw the potential. The pair are trying to keep the business local by employing locals and sourcing local organic produce.
However, the ultimate goal is to take their products worldwide, they said.
"There should be no reason you can't buy Frillys dressing in Hong Kong," said Mr Tomkies.
They are also seeking local investors and will hold a meeting for those interested at 7pm, May 20, at the Masterton Club, 98 Chapel St.
"We are providing an opportunity for investors who do not want to risk a lot of money," said Mr Tomkies.
Coeliac disease is a permanent, autoimmune disorder which causes gluten intolerance.
This causes the body to produce antibodies which damage the lining of the small bowel and make it impossible for the body to absorb vitamins, minerals and other nutrients from food.
Nearly 65,000 people living in New Zealand are affected by the disease, according to Coeliac NZ.
