Vivergo Fuels, owned by Associated British Foods, in Saltend, announced its closure on Friday.
Hull-based Vivergo says all staff will have left and the site will be ready for demolition by the end of the year.
Warburtons is the current market leader and the deal needs approval from the competition watchdog.
Employees and suppliers are warning of a crisis point for the site near Hull amid government talks.
Meld Energy says its plan for a Saltend facility is dependent on Vivergo staying operational.
AB Foods warns it will shut the UK's biggest bioethanol producer unless the government steps in.
Vivergo Fuels has called for government support after the removal of a 19% tariff on US imports.
The plant faces closure after the removal of a 19% tariff on US ethanol imports, bosses say.
Vivergo Fuels, based near Hull, says government support is needed within "the next few weeks".
