This most elegant mosque constructed by Mughal Emperor Shah Jahan on a raised plinth. It is built on an elevated ground, sloping from west to east just in front of the north gateways of the Diwan-i-Khas enclosure. The Khizr Gate (Water Gate) in the east provided entrance from river side for the Mughal nobles and officers, who offered prayers during the period they attended the Imperial court. The river Yununa was very much navigable and the Emperor mostly preferred journey by boat. Even Akbar visited the site for the construction of Agra Fort by boat.
The structure is externally made of red sandstone but the entire interior is finished with white marble. It is one of the first Shah Jahani mosques at Agra in marble after the one built in the Dargah of Hazrat Khawaja Muin-ud-Din Chishti at Ajmer which was built when he was a prince. It is a single quadrangle mosque with a central courtyard which measures 49 m. by 47 m. The mosque (prayer hall) measures 71 m. by 58 m. There is a large tank (hauz) in the centre of the courtyard, which measures 3.5 sq. m.
The arcaded cloisters (riwaq) on the northern, southern and eastern sides measure 11 feet in width with a beautiful gateway in the middle of each one of them. These cloisters are built in marble with typical Shah Jahani pillars and engrailed arches, shaded by projecting eaves. Both the northern and southern gateways consists of ornamental iwans and are crowned by three square chhatris. The eastern main gate is larger and more monumentally composed than the gates in the north and south sides. It is a double storey structure and was the Imperial Gate. There are octagonal towers attached to the corners, which are surmounted by corresponding chhatries. The prayer hall on the western side of the court measures 49 m. by 17 m. It is three bay deep with seven arched openings of cusped arches of Shah Jahani pattern. The facade is protected by wide eaves.
The superstructure of the mosque is remarkable for its magnificent three bulbous domes of Shah Jahani style with seven square kiosks (chhatris) crowning the facade of the building which add much to the height and skyline of the mosque.
A long Persian inscription in elegant Nasta'liq characters inlaid with black marble on the frieze of the facade which eulogises the graceful marble mosque and records its construction by Shah Jahan in seven years (1648-1655) at a cost of rupees three lakhs. As the mosque has the main entrance on the river side, it served as the Jami Masjid for Friday prayers to Mughal nobles and officers beside other dignitaries who came to visit the Daulat Khana of Agra Fort. This fact is borne out by its large dimensions.
That the Moti Masjid is an architectural matchless marvel is emphasised by its inscription which records: "It is a palatial building of paradise made of invaluable pearl for since the beginning of the inhabited world, a parallel of this mosque built entirely of white marble has never been produced since the creation of the world. No place of worship like it resplendid and brilliant from top to bottom has ever appeared before."
The panels in the western wall are finely carved and the floor of the prayer chamber is laid with prayer spaces (musalla) bordered by strips of light yellow marble. On either side are marble screens behind which are the marble panel chambers (Muluk Khana) meant for the Emperor, Princes and other important noblemen.