Involving two young local workers, the pair first approached the Fair Work Ombudsman in 2017, with claims they had been underpaid both in penalty rates and superannuation.
Mooroopna Subway franchise owner Perry Broad said after he became aware of the allegations, he worked with the two individuals to reach a fair outcome with the assistance of the Fair Work Ombudsman.
"The allegations were resolved pursuant to a confidential settlement agreement," Mr Broad said.
"I remain committed to the terms of that agreement.
"I value my hardworking team members and have taken steps to ensure that all employees are receiving fair wages in accordance with the Fast Food Industry Award 2010."
A Subway spokesperson said the company understood the severity of the allegations.
"Like the Fair Work Ombudsman, we are concerned with allegations of wage underpayment," the spokesperson said.
"All franchise owners are expected to comply with employment laws and failure to do so will result in enforcement action and possible termination.
"Subway is undertaking a detailed, independent audit of Mr Broad's restaurant processes and employment records.
"The restaurant continues to be reviewed monthly."
In regards to food safety standard concerns, Mr Broad rejected all claims.
"Food safety is of utmost importance and the restaurant has never served ingredients that do not meet food safety standards," he said.
A Subway spokesperson said the franchise was dedicated to high food safety practices.
"Subway's food safety requirements exceed industry standards and restaurants are frequently audited for food safety," the spokesperson said.
"A dedicated hotline is available to all restaurant employees and Subway investigates any reported concerns swiftly and accordingly."
The Fair Work Ombudsman said it was aware of all allegations and encouraged any workers with concerns to contact the organisation for assistance.
For support, contact the Fair Work Infoline on 13 13 94 or visit fairwork.gov.au