Horticulture Week revealed the administration, with Begbies Traynor of Southend, last week. Around 20 jobs are believed to have gone and the business has closed.
The auctioneers said the sale had come at a bad time of year but they hoped to raise as much as possible for creditors. However, they added that only "a fraction" of the £500,000 worth of stock would be realised. Landlord William Notcutt has taken back the site.
John Woods, a £6m turnover business, formed in 2007 as part of a management buyout from Notcutts Nursery, was regarded as one of the UK’s top five commercial garden centre suppliers and the winner of numerous horticultural industry awards.
The nursery owns the important National Plant Collection of hibiscus plants, recognised by Plant Heritage, together with a collection of mature original ericaceous species, such as rhododendrons and azaleas, from the Waterers Nursery.
The business had run into severe financial problems after several years of difficult trading conditions, and announced a restructuring and creditors voluntary arrangement (CVA) in November 2014.
The nurseries produced more than 1.3 million hardy plants a year on its 65-acre site in Woodbridge, Suffolk. Its 1,500-line product range includes shrubs, perennials, roses, ericaceous plants, climbers, trees and fruit.
The online auction on 24 November is being organised by Eddisons and the lots will be available to view at the John Woods site on Monday 23 November between 10am and 4pm.
Kevin McAndrew, director of machinery and business assets at Eddisons, said: "It’s really sad to see a company like John Woods, which has such a proud heritage in plant growing and gardening being brought down by financial problems.
"The lots that we are auctioning next week will be an opportunity for trade buyers and individuals to pick up some fantastic plants and other items from right across the nurseries’ vast product range."