Bissonnette, 29, pleaded guilty previous year to six counts of murder and six counts of attempted murder in relation to the shooting at the Quebec Islamic Cultural Centre on 29 January 2017.
But he rejected the Crown's request for six consecutive life sentences, which would have prevented Bissonnette from seeking parole for 150 years and guaranteed that he end his life behind bars.
While underscoring the brutality of the attack, Justice Huot suggested that such a harsh sentence would be excessive by denying the defendant the hope of ever leaving prison.
Bissonnette will be eligible to go before the Parole Board of Canada after serving 40 years of his sentence, said Superior Court Justice François Huot. The defence also said it needs time to study the ruling.
The judge read out segments of his 246-page decision as a packed courtroom sat for six hours.
The longest prison sentence in Canada to date is 75 years without parole, which has been given to at least five triple killers including Justin Bourque, who murdered three RCMP officers in a shooting spree in New Brunswick in 2014.
Bissonnette's parents and members of Quebec City's Muslim community were present for the sentencing.
At the start of his trial in 2017, he said he had been suicidal, "swept away by fear and by frightful despair", and deeply regretted his "unforgivable" actions. He noted that Bissonnette's mental health problems contributed to his actions and judged the danger of him reoffending as "moderate" at most.
"His crimes were truly motivated by race and a visceral hatred toward Muslim immigrants", the judge said, adding that his crimes were "premeditated, gratuitous and abject".
Following hearings past year, the sentence was expected to be handed down in October, but the judge delayed it to have more time to ponder his decision.
Several of the mosque shooting survivors and the victims' families also called for consecutive sentences, saying that the lasting trauma of the killing in their community and the horrific crime demands a punishment that is more than 25 years of parole ineligibility. Six people were killed and 19 others were injured.
But Renald Beaudry, a criminal lawyer who was at Bissonnette's sentencing, doesn't think the sentence would be easy to overturn.