Salehi and Ahmadyan were remanded in custody until 23 October when they will appear at the Old Bailey in London.
As part of the investigation, searches were carried out at addresses in Epworth Street, Liverpool, and Lancaster Road, Salford.
The Metropolitan Police said the men are alleged to have obtained instructions to make a chlorine bomb, acquired liquids and other components to make an improvised explosive device and researched and carried out reconnaissance on potential targets.
The prosecution say they carried out “hostile reconnaissance” on buildings in Manchester including the Heaton Park synagogue where two British Jews, Melvin Kravitz and Adrian Daulby, were killed when the synagogue was attacked during last year’s Yom Kippur service, and also at the city’s Jewish Museum.
The court heard the defendants are alleged to have been directed by another Iranian individual who it is believed to be Iran.
