Slavey Slavchev, the Bulgarian owner of EU Plants, now says he will take his dispute with Wokingham Borough Council to the Supreme Court, for which he is seeking the support of the NFU.
The council imposed the TPO on the trees in July 2012 after concluding that pruning on them had not been in accordance with best arboricultural practice.
Earlier this month, Court of Appeal judges ruled that the council was "entitled to be concerned" that the trees' roots might be damaged by continued use of an adjacent unsurfaced track, or if the track were re-surfaced to an inadequate standard.
Slavchev, whose legal fight has cost more than £100,000, said he was "devastated" by the ruling.
He claims to have planted 15,000 native trees and shrubs on the 35-hectare farm, which grows raspberry, blackberry and strawberry plants for commercial growers, since buying it in July 2011.
Slavchev previously came into conflict with his neighbours over the siting of polytunnels on the farm last year, but succeeded in gaining permission for them from the council.