Dudley Muslim Association said instead of a stand-alone dome, the building will have a curved roof and the minaret will stand at 61ft, not 109ft.
It comes despite an on-going battle between the association and Dudley Council over land in Hall Street earmarked for the development. A hearing is due to take place at London's High Court next year.
Outline planning permission was approved for the scheme in 2008 following a planning inquiry. The association had until Saturday to submit a reserved matters planning application to the council.
Bosses have also released a new artist's impression of the scheme. The overall size of the development has been reduced and leaders say it will not be taller than nearby buildings. The changes have been made 'to address people's concerns over the scale and design of the development'.
The association has appointed Al Samarraie of architectural and structural design consultants Archi-Structure, who designs unique places of worship and community facilities.
Mr Samarraie said the current mosque in Castle Hill was no longer suitable for worshippers.
"The community has been at its existing site for over 35 years and the building is not fit for purpose, particularly for women, children, elderly and disabled people," he said.
"The community want to build modern facilities that will be accessible to local people and offer a modern place of worship."
There has been a battle between the association and the town's council over the land earmarked for the mosque.
The association is bidding to stop a buy-back clause in their contract, with the authority forcing the group to sell the land back if building work had not got under way.
Despite losing the first appeal in February this year, Muslim leaders won a second chance to appeal in May.
John Millar, the council's director of the urban environment, said: "The application will go through the normal planning process and will be determined at a future meeting of the council's Development Control Committee."