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Around 60 of the budget outlets are going to close following the Poundland-owned company falling into administration.
The 99p Store locations earmarked for closure are those deemed unprofitable by the parent company, according to Retail Week.
Poundland bought its rival just two years ago and planned to convert 250 of its stores – but now almost a quarter of the original 99p Stores are set to close for good.
Alix Partners is handling the administration.
A spokesperson for Poundland said: “It’s no secret that the previous management of Poundland had difficulties digesting its 99p Stores acquisition.
“However, we’ve largely completed the store closure programme that addressed the remaining overlaps from that 99p acquisition.”
It has not yet been announced which stores will be closing.
99p Stores have gone into administration less than a month after it was revealed Budgens are to close 34 branches.
Budgens is to shut 34 convenience stores with a total of 815 job losses expected. One of the budget shop’s operators, Food Retailer Operations Limited (FROL), has gone into administration.
It also held the leasehold interests in a further 36 non-trading stores, two non-trading properties and the head office of the former Somerfield business.
A statement posted at the announcement said: “Since its acquisition of the stores from Co-op in July 2016, the Company had experienced difficult trading conditions.
“This resulted in the Company being placed into administration despite sustained efforts to make the business more commercially viable.”