Costa Coffee employees at multiple stores claim they have had costs of £200 deducted from their final payslip for training, the BBC has learned.
The BBC spoke to 13 current and former Costa employees at stores in Essex who say they have also been subjected to other deductions for till discrepancies and running costs.
Costa said contracts for franchise stores are managed by partners.
It added some staff contracts did have "clauses relating to deductions".
"Deductions are circumstantial and reviewed on a case by case basis by the partner," a Costa Coffee spokeswoman said.
Courtney Morton was formerly a part-time employee at the Costa Coffee store in Upminster - she earned less than £200 in a week.
Ms Morton was told the deduction for training would be equivalent to one week of pay, and therefore expected to be charged less than £200.
"When I was there I was told that it would be your last week's wages to cover training costs but it turned out to be a flat £200," Ms Morton told the BBC.
And that was not the first deduction she had received.
"The deductions were really unfair," Ms Morton added. "They deducted everyone if they were late, with the money increasing as the time went on up until an hour."
Another former employee, who wished to remain anonymous, said she had one month's pay deducted from her final salary, as well as paying out of her pocket to balance the tills.
Other complaints about the Costa Coffee stores - run by Goldex Investments Essex Ltd - include allegations over contracts.
Six people claim they were never given their written contracts, despite asking for them.
And two people said they were given "promotions" without contracts, claiming that they were carrying out managerial roles while being underpaid for the work they were doing.
Another person, who was promoted to a managerial role, said she was not paid properly for the role she carried out for six months.
Costa Coffee said: "We take complaints such as these very seriously and have shared those we've been made aware of with our partner who operates the franchise business to investigate as a matter of urgency."
The company added: "Anyone you've heard from should get in touch with the partner directly."
Goldex Investments Essex Ltd said it took all the allegations "extremely seriously" and urged employees to outline the issues with their line manager.
Jon Cruddas, the MP for Dagenham and Rainham, said he was writing to the managing director of Costa Coffee UK and Ireland to ensure complaints of "poor treatment of staff - particularly young workers" is dealt with adequately.
He added: "A company that employs thousands of workers across the UK and the branch needs to be held to account."
What is a franchise business?
A franchise is a type of licence that allows a third-party partner to have access and rights to a larger business's logo, name and model, so that the partner can sell a product or provide a service under the business's name.
Claims of unfair deductions were triggered by a Twitter post suggesting that staff at a Costa store were forced to reimburse money lost to scammers who came in to the store.
The Costa Coffee franchise partner, Kafeel Khan, denied he had asked staff to reimburse the scam losses and has since apologised for the "miscommunication" in a letter to the people affected.
The letter was sent after Mr Khan and a Costa Coffee representative arranged a meeting on Friday morning with the father of some of the people employed by Mr Khan.