Matthew Bradbrook of Ravensworth Nurseries, Richmond, North Yorkshire, said more than 600 panes of glass had broken contaminating bedding crops making them unsaleable.
Bradbrook said the glass was insured but explained, "it's not just money, it's getting next year going". Poinsettia, polyanthus and pansy sowing was delayed due to there being no glasshouses usable due to the broken glass.
The greenhouses had to be cleared and re-opened on-by-one and it will be months before the nursery is fully operational again.
The retail shrub area, however, is still operational.
Bradbrook said the storm arrived at around 9pm on 1 July and lasted for only 20 minutes, but left thousands of pounds of damage.
He said: "I've never known anything like it. They [the hailstones] were as big as golf balls."