The service bonus, which gave a £1-per-hour pay increase for teams that scored well, was removed last year. Paid breaks were also removed around the same time, in a bid to cut costs.
However, in April this year as restrictions begun to ease, the Mystery Shopper Bonus was reinstated at a reduced 50p rate.
Then, last week, the sandwich chain told staff that the reduction would be permanent, but has subsequently rowed back on that decision following a backlash.
The removal of paid breaks, however, will not be reversed.
In an email sent to Pret staff late last week, CEO Pano Christou said: "I want to say yet again how grateful I am to every single one of you for the sacrifices that you have made throughout the pandemic.
"The most important thing for me throughout the last year has been to protect as many Pret jobs as we can. However, we also promised to review these changes when our sales improved. As Clare said in her email last week, unfortunately it’s taking longer than we had hoped to get sales back to what they were before the pandemic, which is why we’ve had to make some difficult decisions about how we reward our hard-working teams.
"That’s why in April this year, as restrictions started to ease, we took the decision to return the Mystery Shopper Bonus back to 50p, half of what it was before the pandemic. We also increased the number of contracted hours back to 35 hours.
"We have taken your feedback into consideration, and we’ve reviewed our decision. That’s why we will be returning the Mystery Shopper Bonus back to the pre-pandemic level of £1, effective from the start of September.
"The business is still in recovery but it’s important that we continue to invest in and support our teams however we can.
"I have spent over 20 years working for Pret and spent a long time working in our shops so know how important the Mystery shopper bonus is to everyone and it is something that sets Pret apart from the competition."
The Guardian reported last week that Pret staff were considering strike action over the cut to pay.
Pret has become somewhat symbolic of the financial pain suffered by high-street operators as a result of the Coronavirus crises.
Last summer the chain said the impact of the pandemic had set sales back 10 years, with trade across its 367 high street sites down 60% year on year.
The group has so far been forced to close 36 of its sites, with more than 3,000 employees made redundant.