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Sheikh Hamad bin Jassem bin Hamad al-Thani pleaded not guilty to a series of charges, insisting that he was being "wrongly harrassed".
The full charge sheet read out at Doha's Upper Criminal Court alleged "conspiracy against the state, an attempt to overthrow the emir, collusion with foreign parties, disclosing military secrets and carrying out an attack against the state".
If convicted, Sheikh Hamad and his two co-defendants face the death penalty - though no mention was made of it in court.
The case was adjourned following a request by the defence team to study prosecution documents in greater detail.
More than 120 people have been tried since 1997 for the unsuccessful coup - a mass verdict is expected on 21 December.
Sheikh Hamad was once Qatar's economy minister and the chief of police.
The alleged coup attempt was foiled when Qatari troops overpowered a band of mercenaries on the border with Saudi Arabia, according to the authorities in Doha.
Coup and countercoup
The Emir himself overthrew his father in a bloodless coup in 1995, while the former ruler was out of the country - and Qataris believe the countercoup was intended to restore the old Emir to the throne.
Mystery and intrigue still surround the exact circumstances of how the chief suspect was brought back to Qatar in July.
A source close to the government told the BBC that Sheikh Hamad was "effectively kidnapped" in Beirut and put on a plane to Doha.
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