The 48 suspects are accused of being involved in a suicide bombing at a chapel next to St Mark's Coptic Orthodox Cathedral in Cairo on 11th December 2016 which left 29 people dead.
It is also claimed they are linked to two church bombings in the Nile Delta area on Easter Sunday which claimed 45 lives.
At least 28 people died at St George's Church in Tanta, while another blast at St Mark's Cathedral in Alexandria claimed at least 17 lives.
The incidents prompted a number of churches in the Coptic Orthodox Diocese of Minya in southern Egypt to cancel their Easter celebrations as they mourned the deaths.
The two dozen suspects will also face charges of involvement in an attack which killed eight policemen at a checkpoint in the south-west of Egypt in January.
According to Egypt's chief prosecutor Nabil Sadeq, the suspects joined Islamic State and underwent military training with the group outside of the country.
Egypt has been tackling an insurgency launched by IS-linked militants focused in the north of the Sinai Peninsula. The extremist group recently vowed to continue targeting Christians, who compromise ten per cent of the country's population.