Ray Nethercott is stepping down with immediate effect after surviving a management purge last year, when auditors found a black hole in the accounts caused by problems in the way sales were recorded.
Shares in Allied Carpets fell 3p to 36.5p. Analysts said it was left "rudderless" with just two executive directors, including an acting finance director.
Allied Carpets' chairman, Julian Lee, said he and non-executive director Mark Burgess would now spend more time at the company supporting the remaining two executive directors.
Mr Lee said: "Ray's resignation brings the opportunity for a fresh start for the company and we will announce a successor as soon as practicable." Mr Nethercott is likely to eligible for compensation.
Allied Carpets said trading remained "challenging". In 16 weeks to 16 April like-for-like sales were 6 per cent down on the period last year. This is thought to be in line with the carpet market but a poorer performance than rival Carpetright.
The latest crisis at Allied Carpets could revive bid speculation after the group ended takeover talks last year. However, there may be few bidders.
Carpetright, which made an indicative offer of 67p per share before pulling out due to regulatory concerns, is not thought interested. The company feels it was messed about by Allied over the deal to buy 29 of its stores. The other bidder last year was venture capital group Alchemy.