Jones said that one person called out "it's f***ing bull***".
Another screeched their car's tyres as they raced out of the carpark. The police were called after the car nearly hit another vehicle as it left.
In a post on Facebook the bakery stated, "this is not our choice, we did not make up these rules, we have done what's best for our business and staff and customers wellbeing - we can't survive on takeaways alone".
"Please do not upset our girls they are only doing what they are told."
Jones described the two instances as "not fun" but she had expected "it wasn't going to be smooth sailing".
The Rustic Bakery in rural Canterbury made the decision to only serve vaccinated customers "as it keeps the business the safest".
Every customer had to show their vaccine pass to prove they were double-vaccinated before they were served.
Customers also had to sign in or scan the shop QR code and wear a mask.
Jones said "95 to 98 per cent of the customers have been great this morning".
"It's has been a long time coming, we are following the law and we would like to keep our jobs".