The move comes after the company was "named and shamed" by the UK government.
The Department for Business Innovation and Skills published a list of companies which were found to have failed to pay the legal minimum.
G1 Venues, which is run by entrepreneur Stefan King, was one of the biggest offenders.
It was found to have underpaid staff by more than £45,000.
The government statement said that the part of the chain affected was the Arta restaurant in Glasgow's Merchant City.
G1 Group issued a statement explaining that it deducted pay from staff for uniforms and for training intended to help their career.
It said: "We understand that in effect, this has previously brought some employees marginally below the minimum wage in some pay periods.
"For this reason, we no longer apply these deductions, and any associated repayments have been made in light of this issue being highlighted."
The company added: "We are extremely focused on the protection, training and development of our staff, from junior roles on national minimum wage all the way through to senior management levels.
"A fundamental part of this process is our annual pay scale reviews - ensuring our employees are always paid in accordance with minimum wage guidelines."
G1 is one of Scotland's biggest leisure chains, with more than 40 venues. These include the Corinthian Club and Grosvenor Cinema in Glasgow, Perth Playhouse and Ghillie Dubh in central Edinburgh.
In October 2013 the government revised rules allowing it to publicly name companies that have been found to breach wage laws.
Since that time, a total of 210 companies have been accused of wage theft, after investigations by HMRC.
In total, those firms owe some £635,000 to workers, as well as fines of nearly £248,000.
Business minister Jo Swinson said: "There's no excuse for companies that don't pay staff the wages they're entitled to."
Glasgow-based leisure chain G1 has ended the deduction of wages to pay for uniforms and training.