Skylights were added to let in more natural light, which together with lighting sensors and controls, have reduced the required amount of artificial lighting in the store.
Air conditioning was replaced with free cooling in summer, beer and wine fridges had doors fitted, and chest freezers were given lids.
The end result has been a 40 per cent energy saving, equating to "a big number" in terms of dollars, which Jones has passed on to customers in product prices.
Jones said he and Ecosystems had not come up with any new ideas, but simply took a number of separate ideas being used in other supermarkets.
"We probably only broke new ground because we have been the first supermarket in New Zealand to put them all together."
Ecosystems CEO Grant Robertson said he was proud of his company's work at the store but the real praise goes to Jones for responding to his son.
"Really it's a huge accolade for the owner Gareth Jones because any changes that impact on the customer are a risk.
"By putting a lid on the freezers and doors on fridges, you put a barrier in between the product and customer. That's quite courageous."
Award judges said "it was a brave move" by Jones to take on consumer behaviour.
"This sets a real benchmark across the industry. It scores high on all criteria - everyone wins, including customers," the judges said.
Ecosystems is now in talks with the Foodstuffs Group about upgrading stores nationwide to increase sustainability, Robertson said.
The Supreme Award was given to Air New Zealand, which reduced fuel use by 15 per cent and cut CO2 emissions by 142,000 tonnes per year.
EECA said that across all awards entrants, the value of energy saved or generated over the life of the projects is $600 million, and the total CO2 emissions reduced or avoided is 1.7 million tonnes.