The Durham all-rounder, who missed the Ashes after being suspended from playing for England, is accused of affray with two other men.
A 27-year-old man allegedly suffered a fractured eye socket in the incident, at which fellow England cricketer Alex Hales was also present.
England cricketer Ben Stokes on Monday pleaded not guilty to charges of affray following an incident in Bristol last September and he will face trial on August 6. The second Test against India starts on August 9.
Stokes, 26, wearing a grey shirt, said "hi judge" when he was introduced to Judge Peter Blair QC via the video link.
Stokes is being represented by Mr Gordon Cole, Hale is being defended by Michael Hall and Ali by Giles Nelson.
The trial date has been set for 6 August and the three defendants were granted unconditional bail.
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According to the Islamic Republic News Agency, IRNA, British police did nothing to protect the compound during the attack . Police have ordered reinforcements around all diplomatic missions in the city.
Stokes was present in court to issue his not-guilty plea and confirm his identity as his trial preparation hearing got underway in Bristol.
Stokes this weekend helped England win a one day series against New Zealand.
He will, however, be able to play for Rajasthan Royals in the Indian Premier League in April and May.
Stokes was told he "must be here for your trial" and all three defendants were advised to provide defence statements by May 22.
Mr Stokes, Mr Hale and Mr Ali were detained early on 25 September following a disturbance in the Clifton Triangle area of the city - several hours after England had played a one-day worldwide against the West Indies. Hales faced no charges.