Magnotta will also be tried on four other charges, including causing indignity to Lin's body, broadcasting obscene material, using the postal service to send obscene material and harassment of Prime Minister Stephen Harper and other members of Parliament.
A trial date will be set on April 29.
Last year, the 30-year-old Ontario native pleaded not guilty and opted for trial before a judge and jury.
The weeks-long preliminary inquiry in the case wrapped up earlier today at the Montreal courthouse. Evidence presented at that hearing cannot be published because of a court-ordered ban.
Judge Lori Renée Weitzman, who heard from more than 30 witnesses in recent weeks, has ruled there is enough evidence to proceed to trial in the case.
Earlier this week, Magnotta's lawyer told the court that if his client is ordered to stand trial, it should be on a lesser charge.
Luc Leclerc, who is representing Magnotta, told the judge that the Crown must show that the killing was both planned and deliberate for a charge of first-degree.
He said based on his analysis, the judge cannot conclude the evidence presented at the hearing justifies that charge.
Magnotta stands accused in the killing and dismemberment of Lin, a Chinese national. He was arrested on June 4, 2012, in an internet cafe in Berlin, Germany, after an international manhunt.