Shares in the company that owns Poundland, Benson for Beds and Harveys have slumped after the South African business revealed it was launching an investigation into accounting irregularities.
Its European operation expanded previous year to include United Kingdom discount retailer Poundland.
That report said Jooste is among employees being investigated by German prosecutors in a 2015 case linked to possible accounting fraud.
Late on Tuesday, Steinhoff announced that it had approached professional services multinational PwC to carry out an independent investigation of the irregularities. In addition, the Company will determine whether any prior years' financial statements will need to be restated.
Markus Jooste, chief executive of German-listed Steinhoff International Holdings NV, has resigned, the company said on Tuesday.
As well as furniture and homeware, it also sells products including clothing, footwear and consumer goods.
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The company's chairman, Christo Wiese, will become executive chairman on an interim basis.
Its brands include Bensons for Beds and Harveys in the UK, Conforama in Europe, Pep and Ackermans in South Africa and Snooze in Australia.
It bought Poundland previous year and has introduced its Pep&Co budget clothing brand into scores of stores.
Steinhoff's holding company is based in Amsterdam for tax reasons and has its primary listing on the Frankfurt stock exchange.
"The supervisory board of Steinhoff wishes to advise shareholders that new information has come to light today which relates to accounting irregularities requiring further investigation", the statement said.
It is not now clear what "accounting irregularities" the company is referring to in its statement.