The architecture of the mosque has a heavy influence of both Islamic and Italian. Designed by an Italian architect, the mosque is constructed on an artificial lagoon near the banks of the Brunei River circulated by a water village named Kampong Ayer. The Sultan Omar Ali Saiffuddin mosque consists of marble minarets and golden domes with courtyards and fertile gardens filled with fountains. The mosque is circulated by a plethora of trees and floral gardens which in Islam it is considered as an interpretation of heaven. It also has a long bridge meandering across the lagoon to Kampong Ayer the water village. Also, there is another marble bridge connecting to a structure in the water that resembles a ship was at one time used for official state ceremonies.

The main dome which is thought to be the mosque's most recognisable feature is covered in pure gold. The mosque stands at 52m (171ft) high and can be seen from virtually anywhere in Bandar Seri Begawan. The main minaret is the mosque's tallest feature. It incorporates a Renaissance and Italian architectural style which is a unique theme seen in few Islamic houses of worship across the world. The minaret has a working and modern elevator which goes to the top of the structure, people who reach the top of the minaret can witness a panoramic view of the city. The interior of the mosque is for prayer only but it has a magnificent mosaic stained glass, as well as many arches, semi-domes and marble columns. Nearly all the material used in the construction of the building has been shipped in from other countries. For example, the marble is from Italy, the granite from Shanghai, the crystal chandeliers from England and the carpets from Saudi Arabia. Hence, the Sultan Omar Ali Saiffuddin mosque has become the sultanate's prominent architectural achievement and the main tourist attraction in the country and Asia as a whole.