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.
The January 2017 shooting, which Prime Minister Justin Trudeau denounced as a "terrorist attack", provoked debate over the treatment of new arrivals at a time when a growing number of migrants crossed from the United States into the province of Quebec.
The attack at the Quebec Islamic Cultural Centre in the quiet Sainte-Foy neighbourhood of Canada's oldest city, he concluded, will go down in Canadian history "written in blood" as one of this country's worst tragedies.
CORRECTION: A previous version of this story incorrectly reported that Alexandre Bissonnette had already been sentenced to life in prison, with no chance of parole for 35 years. Even if the judge decides the sentences should be served concurrently, it does not necessarily mean Bissonnette would walk out of prison after 25 years.
He also lacked empathy, the judge said, quoting Bissonnette's statement after the shootings: "I regret not having killed more people".
He will learn his fate at the Quebec City courthouse in a ruling by Superior Court Justice Francois Huot.
But Huot said Bissonnette had previously considered attacking other targets including feminists, shopping centres and airports.
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. The sixth attempted murder charge related to others who were nearby in the mosque.
The longest sentences to date in Canada is 75 years without parole, which has been handed down in five cases - all involving triple murders.
Like the rest of the world, Islamophobia has become a problem in Canada.
In pleading guilty, Bissonnette expressed shame and remorse for his actions but offered no clear explanation of why he did it. "I am not a terrorist, I am not an Islamophobe".
"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.
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.
Under Canadian law, Bissonnette could have gone to prison for 150 years or 25 years for each of the six deaths.