The accused is facing a first-degree murder charge and four other charges in the death and dismemberment of Chinese student Jun Lin in May 2012.
The 31-year-old accused entered the pleas in a low voice while in a glass-enclosed prisoner' box at the Montreal courthouse.
Standing up, Magnotta uttered "not guilty" five times as the charges were read out loud by the clerk.
The four other charges are: committing an indignity to a body; publishing obscene material; criminally harassing Prime Minister Stephen Harper and other members of Parliament; and mailing obscene and indecent material.
While Magnotta had already pleaded not guilty to the charges in a lower court in June 2012, murder trials are heard exclusively in Quebec Superior Court, where he appeared Wednesday.
His jury trial is set to begin next September and be presided by Justice Guy Cournoyer.
Cournoyer rejected a motion from defence lawyer Luc Leclair on Wednesday for a publication ban on certain aspects of the case.
Leclair wanted to stop the media from reporting that his client has often been shackled and handcuffed in court and that he has frequently appeared in a high-security courtroom.
The lawyer argued the description would make it difficult to find an impartial jury and hamper his client's right to a fair trial. He wanted the ban to take effect until the trial next year.
Cournoyer denied the motion, saying there was insufficient evidence to prove the publication of such information would deprive Magnotta of a fair trial.
The Crown and media lawyers didn't see the need for the request in the first place.
"I'm convinced that you can find 12 impartial people who will be able to hear this case," said Mark Bantey, a media lawyer who argued against the ban.
"When your'e looking for an impartial jury, you're not looking for people with no knowledge, you're looking for people who can be impartial and decide the case solely on the basis of the evidence... Our whole system is based on that."
Cournoyer will hear several other trial-related motions between now and when the case is heard. The next hearings are scheduled for Feb. 6 and 7.
The judge noted the trial will begin Sept. 8, a week ahead of schedule.
It could last between six and eight weeks.
Magnotta was dressed in black and looking a bit heavier than when he was arrested. He sat quietly and listened to proceedings, occasionally using a telephone from inside the enclosure to talk with his lawyer.
The former stripper and porn actor from Scarborough, Ont., was arrested in Berlin in June 2012 following an international manhunt that made headlines around the world.
In the past, Lin's family has come from China to attend the hearings. On Wednesday, a lawyer representing the family was in court, taking notes.
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