Ordered by Sultan Bayezid I, the mosque was designed and built by architect Ali Neccar in 1396–1400. It is a large and rectangular building, with a total of twenty domes that are arranged in four rows of five, and are supported by 12 columns. Supposedly the twenty domes were built instead of the twenty separate mosques which Sultan Bayezid I had promised for winning the Battle of Nicopolis in 1396. The mosque has two minarets.

Inside the mosque there are 192 monumental wall inscriptions written by the famous calligraphers of that period. There is also a fountain (şadırvan) where worshipers can perform ritual ablutions before prayer; the dome over the şadırvan is capped by a skylight which creates a soft, serene light below; thus playing an important role in the illumination of the large building.

The horizontally spacious and dimly lit interior is designed to feel peaceful and contemplative. The subdivisions of space formed by multiple domes and pillars create a sense of privacy and even intimacy.

The mosques that were built after the conquest of Constantinople (Istanbul) by the Ottoman Turks in 1453, and influenced by the design of the 6th century Byzantine basilica of Hagia Sophia, had increasingly elevated and large central domes, which create a vertical emphasis that is intended to be more overwhelming; in order to convey the divine power of Allah, the majesty of the Ottoman Sultan, and the governmental authority of the Ottoman State.