In the end, he sentenced Bissonnette to concurrent life sentences for five murders, and on the sixth added 15 years to bring the total to 40.
While first-degree murder carries an automatic life sentence, Huot said he had to decide how long Bissonnette would have to wait before he could ask for parole.
One of the man's victim who was paralyzed in the attack, Aymen Derbali, said that numerous survivors were not pleased with the judge's sentencing.
Bissonnette walked into the Quebec City Islamic Cultural Centre on January 29, 2017, opening fire with a nine-millimetre pistol.
Alexandre Bissonnette, a suspect in a shooting at a Quebec City mosque, arrives at the courthouse in Quebec City, Quebec, Canada, February 21, 2017.
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.
"Charter challenges to the 2011 provisions had previously been denied on the basis that the judge was not forced to increase parole ineligibility for multiple murders, " he wrote in an email to The Canadian Press.
This was a Reuters error as the judge was still reading his judgment.
The victims were brothers Ibrahima Barry, 39, and Mamadou Tanour Barry, 42, Khaled Belkacemi, 60, Aboubake Thabti, 44, Abdelkrim Hassane, 41, and Azzedine Soufiane, 57.
Silver agreed that the Bissonnette sentencing is also likely to be appealed, and she believes that's a good thing.
On the other hand, the judge said, Bissonnette had no previous criminal record, he pleaded guilty and he expressed remorse.
Six people were killed and 19 others were injured.
People hold candles for victims of Sunday's deadly shooting at a Quebec City mosque, during a vigil in Montreal on Monday, Jan. 30, 2017.
The crime prompted an outpouring of horror and sympathy that reached across Canada and around the world, prompting a wider conversation on Islamophobia, intolerance, and the need for better understanding between communities.
But in a police interrogation, Bissonnette told investigators he wanted to protect his family from terrorists when he committed the killings.
"No matter the outcome of today's decision, nothing can diminish the incredible support & solidarity felt by many Canadian Muslims in the wake of the attack, and during the past 2 years", the group said on Twitter.
However, Huot said under Canadian law he could only decide in 25-year tranches on parole, CBC News' Catou MacKinnon reported, and 50 years was "clearly excessive".