South Lanarkshire Council has said it is satisfied that Errington Cheese Ltd now has the relevant controls in place.
The firm's Dunsyre Blue variety was linked to an E.coli outbreak last July in which a three-year-old girl died.
The company - which is now producing cheese under a revised food safety management system - disputes that its products were responsible.
The Carnwath-based firm's new season Lanark Blue cheese has now been put on the market.
A total of 11 people received treatment in hospital during the E.coli outbreak in the summer of 2016.
In September, Scotland's Food Safety watchdog, Food Standards Scotland (FSS), imposed a ban on all cheese produced by Errington. People were advised not to eat the cheese and to return it to the seller.
In January, Errington won the latest round of a court battle against the sales ban.
The interim order was designed to force the council to either abandon the case against them or initiate new proceedings under food hygiene regulations.
In February, a batch of cheese was seized by officers from South Lanarkshire Council but later that month the council announced it was allowing the sale of the Corra Linn cheese.
Food Standards Scotland said that decision was "premature" and warned people not to eat it.
On Thursday, Food Standards Scotland said South Lanarkshire Council had provided the necessary assurances that the cheese products covered by the Food Alert For Action issued in September 2016, and revised in November 2016, had either been destroyed or seized to protect public health.
The agency said it could not comment further due to ongoing legal proceedings.
A South Lanarkshire cheese company at the centre of an E.coli outbreak has restarted production.