Jaser is facing four terrorism-related charges while Esseghaier is also facing a fifth terrorism-related charge.
Judge Michael Code told jurors he wants them to try and reach a verdict on all counts, CBC's Laura Lynch reported from court in Toronto.
The judge told the jurors before they began their deliberations last week that the most important evidence in the case was 25 hours of secretly recorded conversations between the accused and an undercover FBI agent.
The officer posed as a wealthy Egyptian-American real estate developer whose views had supposedly become more hardline in recent years and who was a willing accomplice in the alleged conspiracy.
He rented a "safe house," which had been bugged by police, for the operation. And he bought the two accused plotters meals, drove them to scouting locations and handed out cash.
The court heard conversations in which Jaser and Esseghaier discussed their ideologies, the alleged plot to derail a Via Rail train travelling between New York and Toronto and other ideas for potential attacks, including Jaser’s alleged "sniper plot" idea, which would have been in retaliation for Canadian military actions in Muslim countries.
Jurors were also shown aerial surveillance of the two accused and the undercover officer scouting a railway bridge in September 2012 in broad daylight as several trains passed by only metres from the men.
The trip drew attention and the men were stopped after they had returned to their vehicle by uniformed Toronto police officers who were unaware the men were under surveillance. The FBI agent told officers they were sightseeing and the men were given a warning.
Esseghaier didn’t participate
Jaser’s lawyer argued that he was only pretending to be interested in the plan as part of an elaborate scheme to extract money from Esseghaier and the undercover officer.
Jaser, a Canadian permanent resident of Palestinian descent, pleaded not guilty. He did not testify in his own defence.
Esseghaier, a Tunisian national who was pursuing a PhD in Montreal when he and Jaser were arrested in April 2013, chose not to participate in his trial, because he wanted to be judged by the rules of the Qur'an.
He did not cross-examine any witnesses or bring a defence, but he did offer the jury what he considered "sincere advice" in an usual written closing statement, urging them to follow the rules of the Qur'an and prepare for "judgment day."
He had a not-guilty plea entered by the judge.