Wahaca has tightened up its policy on walk-outs, after a waiter was told to pay part of the bill when his customers left without paying.
The company said waiters would no longer have to pay any element of the bill when this happens.
However, if a manager suspected the waiter was "complicit" in a walk-out, this would be investigated, it said.
The restaurant chain previously only made servers cover part of the bill in rare cases of "real negligence".
Wahaca said this was not the case when a waiter in a London branch was asked by the manager to pay £3 towards a £40 unpaid bill.
The waiter has now been assured he will not have to pay, after a customer raised the issue on Twitter.
Sarah Hayward, a former Labour leader of Camden council, tweeted that she was eating at Wahaca in Kentish Town when she witnessed the eat-and-run incident.
She told the BBC that the waiter then informed her he would have to cover the cost of the bill, prompting her to express her concerns on social media.
Hi @wahaca just eaten in your Kentish Town restaurant for the last time.— Sarah Hayward (@Sarah_Hayward) June 15, 2019
Ppl next to us left without paying and their server is made to foot the bill from his wages. Apparently company policy. Utterly shameful employment practice.
Food's great, company is crap.@thomasinamiers
Wahaca said the incident was caused by an "internal communications issue" which has now been resolved.
Co-founder Mark Selby told the BBC that in light of the incident, the company had decided its policy needed a "clearer direction".
Previously, the procedure was that an individual should only be held accountable for an unpaid bill in cases of "real negligence" - where they allowed a customer to leave, knowing they had not paid.
That decision was down to the discretion of the manager, but the amount was generally 10% of the net bill minus VAT - or 30% of the food bill - Mr Selby said.
The new policy will mean waiters will not have to pay any element of the bill if a table they are responsible for leaves without paying.
However, if the manager suspects the waiter was "complicit" in the walk out - for example if they were friends with the customer and the server knew they intended not to pay - there would be a full investigation and the operations manager would decide the appropriate action, Mr Selby said.
Wahaca said its policy is in line with industry standards.
A spokesman for the union Unite, Alex Flynn, said the incident which prompted the policy change was "outrageous".
"Hospitality staff are already paid a low wage, but to then be expected to pay for the dishonesty of customers is quite shocking," he said.
Mr Flynn said the union had also received reports of similar cases in other chains.
Where service charge is paid by card, rather than in cash, he said restaurants often used this money to cover the bills of customers who had left without paying, leaving the staff member with less money in tips.
The Wahaca chain was founded by Mr Selby and 2005 Masterchef winner Thomasina Miers in 2007 and now has 25 branches across the UK.