The program, set up by not-for-profit organisation Responsible Runners, encourages cafes to offer a discount to customers who bring a reusable cup for their daily coffee.
Mayor Giovanni Italiano said Australians discarded one billion cups and lids each year.
"This is just unsustainable and we are encouraging cafes to sign up and be the change for a cleaner world," he said.
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READ NOW"We aim to have a minimum of 30 cafes within the City's boundaries signing up by the end of June next year."
Dome Osborne Park was one of the first cafes to sign up to the program.
Franchisee operator Jennifer Methven said she felt it was important to be a part of a more sustainable way of serving and purchasing hot drinks.
Cafes that sign up to the program before June 19 will receive free reusable coffee cups from the City to give to their customers, while those that sign up this year will be provided with a pack from organisers.
Cafes interested in taking part can register at www.responsiblerunners.|org with no direct costs to be part of the program.