The former Wales skipper was arrested last month near his home at Redbourn, Hertfordshire, just before midnight on 11 November.
Jones, 32, appeared at St Albans magistrates' court dressed in a smart dark suit.
He was charged with assaulting 27-year-old Timothy Gear and of causing criminal damage to a kitchen window and the door of a mobile home near his 60-acre farm.
During the seven-minute hearing, Jones, who sat next to his solicitor, spoke only to confirm his name and address. His wife Tanya watched from the public gallery. The case was adjourned until 7 January.
Jones, his wife and his advisers left the court declining to comment on the charges.
Jones is a controversial player who has a reputation for being one of the hard man of football. He has clashed with the authorities on a number of occasions and been fined by the Football Association for presenting a video on foul play.
On the plus side, however, his commitment to the cause and under-rated skills have been talismanic for a number of clubs.
Apart from Wimbledon, Leeds, Chelsea, and Sheffield United have all benefited from his presence in their ranks.