Mustafa Zanibar, 32, was already serving a 29-year prison term for murder when Judge Baltasar Garzon accused him of forming part of an Islamic group planning to blow up high-profile buildings in Madrid including Real Madrid's football stadium.
The alleged Martyrs for Morocco plot to blow up the High Court with a truck bomb was discovered late last year and several arrests followed, but some of the suspects were already in jail for other offences.
Zanibar, who had been isolated since Garzon's accusation, was found hanging in the shower at a prison in Zaragoza on Thursday, a spokeswoman for the prison service said.
She added he was thought to be linked to Muhammad Ashraf, the spiritual leader of the Martyrs for Morocco, who is being held in Switzerland for alleged immigration violations.
Dozens of suspected Islamist activists have been arrested in
the last year, either for a suspected role in the 11 March 2004 train bombings in Madrid, in the 11 September 2001 attacks, or in the thwarted attack on the High Court.
However, human rights groups say Spain's counter-terrorism measures infringe on basic human rights.
In a recent report, New York-based Human Rights Watch cited incommunicado detention and secret legal proceedings, limitations on the right to a lawyer during the initial period of detention, and lengthy periods of pre-trial detention.
"Spain is right to tackle terrorism through the criminal courts. But the government needs to ensure that terrorism suspects have the due process rights necessary for an effective defence"
Human Rights Watch
Rachel Denber, of Human Rights Watch, said in the report: "Spain is right to tackle terrorism through the criminal courts. But the government needs to ensure that terrorism suspects have the due process rights necessary for an effective defence."
She added: "The victims of the horrific 11 March bombings, and all victims of terrorism, have the right to see the perpetrators brought to justice.
"Spain has an obligation to protect its citizens from such acts, but it also has a duty to respect fundamental rights while doing so, including the due process rights of those charged with acts of terrorism."