The dark-haired, slightly-built Bissonnette, who wore a white shirt under a navy blue jacket and handcuffs, had been described by police as a lone-wolf attacker.
The Crown had recommended that the 29-year-old Bissonnette serve six consecutive sentences totalling 150 years.
The six men killed were Ibrahima Barry, Mamadou Tanou Barry, Khaled Belkacemi, Abdelkrim Hassane, Aboubaker Thabti and Azzeddine Soufiane. More than 50 people were at the Quebec Islamic Cultural Centre in January 2017 when he began shooting during evening prayers.
The killer's "highly premeditated" attack on the mosque will go down in Canadian history "written in blood" as one of this country's worst tragedies, Huot said in court.
Alexandre Bissonnette, 29, will be eligible for parole in 40 years. Hout ruled on a life sentence with the eligibility of parole only after 40 years.More news: Toronto serial killer given life in prison for murdering eight
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He also lacked empathy, the judge said, quoting Bissonnette's statement after the shootings: "I regret not having killed more people".
Prosecutors had said that Alexandre Bissonnette's crime was so hateful and so obviously motivated by bigotry that he should receive the maximum penalty of 25 years for each of the victims the 29-year-old murdered on the night of January 29, 2017.
Justice Francois Huot discarded the prosecution's proposal, however, calling it "unreasonable" and that allowing a prisoner to die in jail would be "cruel and unusual punishment" and contrary to Canada's Charter of Rights and Freedoms. Specifically, the attack came days after President Donald Trump announced his Muslim immigration ban and Justin Trudeau responded by saying Canada is open to refugees. The sixth attempted murder charge related to others who were nearby in the mosque.
The longest prison sentence in Canada to date is 75 years without parole, which has been given to at least five triple killers since the law was changed to allow consecutive sentences.
In pleading guilty, Bissonnette expressed shame and remorse for his actions but offered no clear explanation of why he did it. Several of the survivors and the victims' families have argued for a sentence longer than 25 years, noting the heinous nature of the crime and the lasting trauma it caused for the Muslim community. They called a 150-year sentence the equivalent of a "death sentence by imprisonment" and said it would be "contrary to human dignity".
But Renald Beaudry, a criminal lawyer who was at Bissonnette's sentencing, doesn't think the sentence would be easy to overturn.