Seventy-four people were killed in the attacks in 2016 and 2017 targeting Coptic Christians in Cairo, Alexandria and the Nile Delta city of Tanta.
The court also sentenced 19 people to life in prison and 10 others to between 10 and 15 years, judicial and security officials said.
Christian sites of worship across Egypt have been repeatedly targeted in attacks claimed by IS, prompting the authorities to impose a state of emergency 18 months ago.
A suicide attack on December 11, 2016 on the Saint Peter and Saint Paul church killed 29 in the heart of Cairo.
The following April, 45 people were killed as Christians gathered to celebrate Palm Sunday in the cities of Tanta and Alexandria.
Coptic Christians make up about 10 percent of Egypt's predominantly Sunni Muslim population.
Since the military overthrow of Islamist president Mohamed Morsi in 2013, hundreds of police officers, soldiers and civilians have been killed in jihadist attacks.
In November last year, suspected IS militants killed more than 300 Muslim worshippers in a gun and bomb assault on a mosque in the Sinai Peninsula.
The Egyptian army is waging a major operation focused on the Sinai aimed at wiping out IS.
In April, a military court had initially condemned 36 people to death over the church bombings.
The retrial came after the case was referred to the Grand Mufti, Egypt's highest religious authority, as required by law whenever a death sentence is passed.