The suspects are accused of "preparing a crime to threaten the life or health of many people or property" using explosives.
They were also charged with "public incitement to murder against ethnic and religious groups", possession of explosives and firearms without a permit, and the transport of drugs within the European Union.
They face prison sentences of up to 10 years if convicted.
Authorities say the attack was planned for a "specific religious object of the Islamic community" and the perpetrators had also planned to "spread poisonous substances".
Prosecutors in Szczecin brought charges against the two last month, following a joint investigation led by Poland's Internal Security Agency.
The two suspects had planned to "prevent the Islamization" of Poland, the authorities added in a statement.
Both defendants are said to have prevented "extreme views", calling for violence and Islamophobia. One of the two also created a "manifesto", similar to one written by the far-right terrorist in the Christchurch mosque attacks in 2019.
The "manifesto" included calls for the persecution of newcomers from outside Poland, including the use of firearms and explosives, the authorities added in a statement.
The two suspects were arrested in Warsaw and Szczecin by the Internal Security Agency in November 2019 and both had been under surveillance since 2013.
During the investigation, four firearms, including a homing machine gun and ammunition, and explosives were seized, alongside "tools enabling the production of hazardous materials and substances".
A spokesman for the Minister of the Special Services Coordinator added that one of the suspects had been "producing" firearms, ammunition and explosives despite a previous court order, Euronews reported.
Also recovered were "eight vials with highly toxic chemicals" and more than 170 books on the production of explosives, as well as electronic data carriers that can be used to maintain encrypted communication.
A third individual was also charged with possessing explosives precursors without a permit, an offence which is punishable by up to 2 years imprisonment.