The construction of the mosque first began in 1597. It was ordered by Safiye Sultan, who was the wife of Sultan Murad III. The original architect was Davut Aga, an apprentice to the great Mimar Sinan. However, Davut Aga died in 1599 and was replaced by Dalgic Ahmed Cavus.

The project was hampered by political disconnect, and its location and monetary implications created dissent in the court. The Eminonu neighborhood was the city's foremost commercial center, and home to a predominantly Jewish population. In situating the mosque there, Safiye Sultan hoped to extend the sphere of Islamic influence within the city, capitalizing on the growing discontent of local and foreign merchants caused by the growing power and influence of their Jewish counterparts, which gave the Sultan an easy justification for confiscating their property. However, the vast monetary outlay drew sharp criticism. In particular, the Janissaries resented the growing political power of the Valide Sultan, and believed the mosque to be an unnecessary expenditure. Safiye Sultan was forced to abandon the project upon Mehmet III's death. The new Sultan Ahmed I had no interest in pursuing the project after Safiye Sultan was relegated to the harem and the construction was abandoned.

The partially constructed structure fell into ruins and was largely destroyed by a fire in 1660. Later that year, the imperial architect Mustafa Aga suggested that Valide Turhan Hadice, mother of Sultan Mehmet IV, should complete the project as a work of piety. The mosque was finally finished in 1663, and inaugurated in 1665.

Exterior

The exterior of the mosque itself boasts sixty-six domes and semi domes in a pyramidal arrangement, as well as two minarets. The main dome measures thirty-six meters in height, and is supported by four flanking semi-domes. The dome plan of the New Mosque is based on the earlier Sinan's Sehzade Mosque and Sedefhar Mehmet Aga's Sultan Ahmed Mosque.

As with other imperial mosques in Istanbul, the mosque itself is preceded by a monumental courtyard (avlu) on its west side. The courtyard of the New Mosque is 39 meters on a side, bordered on its inner side by a colonnaded peristyle covered by 24 small domes. An elegant sadirvan (ablution fountain) stands in the center, but is only ornamental. The actual ritual purifications are performed with water taps on the south wall of the mosque. The façade of the mosque under the porch is decorated with İznik tiles. Stone blocks supplied from the island of Rhodes were used in the construction of the mosque.

Interior

The interior of the mosque is a square 41 meters on each side. The central area is defined by four large piers which are the main support for the dome. On the sides and rear of the central area are colonnades of slender marble columns connected by arches in a variety of styles. The dome is 17.5 meters in diameter and has a height of 36 meters. The interior space is extended with semi-domes along the east-west axis of the building, with smaller domes above each corner of the nave and even smaller domes above the corners of the galleries.

The northeast corner of the gallery has a gilded screen, behind which members of the imperial court could attend services. This Royal Loge is connected by a long elevated passageway to a Royal Pavilion in the northeast corner of the mosque complex.

The interior of the mosque is decorated with blue, green and white İznik tiles, which are considered somewhat inferior in quality to tiles in earlier imperial mosques. The mihrab is decorated with gilded stalactites and the mimbar had a conical canopy with slender marble columns.

Complex

       

As with other imperial mosques in Istanbul, the New Mosque was designed as a kulliye, or complex with adjacent structures to service both religious and cultural needs. The original complex consisted of the mosque itself, a hospital, primary school, public baths, Turbe, two public fountains and a market. To this complex was added a library during the reign of Sultan Ahmet III.

The large L-shaped market survives today as the Egyptian Bazaar (also known as the "Spice Bazaar"), a well-known Istanbul tourist attraction.

The mausoleum (turbe) holds the graves of the Valide Sultan Turhan Hadice, her son Mehmet IV as well as five later sultans (Mustafa II, Ahmet II, Mahmut I, Osman III and Murat V) and various members of the court.

Ongoing restoration and maintenance works are implemented by the Turkish General Directorate of Foundations.