Under the guidance of Orthodox Metropolitan Bishop Amvrosios of Kalavryta, clerics in his diocese decided that, from Sunday, the bells would ring every day at noon for three minutes until Saturday.
The decision follows Greece's parliament passing the bill - backed by Prime Minister Alexis Tsipras - with 171 votes in favour in Greece's 300-seat parliament last week.
The Orthodox Church said in a statement that the change in law was "a satanic deed" and would lead to "the destruction of social cohesion and the spiritual necrosis of man".
Greeks over the age of 15 will now be able to change the gender listed on their identity cards and other official documents following a simplified procedure in court.
The Church is continuing to call for the bill to be withdrawn.
A statement obtained by the AP, by the Kalavryta diocese's clerics on Saturday read: "It is an outrageous inspiration for someone to change his gender in a few minutes, with a simple declaration, so contrary to what God has gifted people with ... whoever has 'gender dysphoria' is mentally ill.
The statement also said homosexuality is a "deadly sin" and expressed a worry that legislation allowing adoption by same-sex couples would be next.
The clerics have also said they will display protest banners in the city of Aigion, which is the largest in the diocese.