The current mosque likely follows the 12th century Kara-Khanid footprint, measuring 130 x 80 meters. Unfortunately we know little about the layout of the Kara-Khanid era mosque and its predecessors; the present floor plan was likely derived from Timurud-era precedent such as the the Bibi Khanum mosque of Samarkand, built in 1399. Both buildings feature a four-iwan plan, a large interior courtyard, a high dome over the mihrab, and deep hypostyle halls vaulted in hundreds of small domes—288 in all at the Kalyan Mosque.

The east-façade entrance features a monument iwan with a half dome; the exterior surface is covered with elaborate and costly mosaic faience tiles. On the opposite end of the building is a mihrab—a niche facing Mecca—surrounded with tilework signed by its creater, Bayazid Purani. The domed chamber in front of the mihrab is complemented on the exterior by a blue-tiled dome set upon a high drum wrapped in kufic calligraphy. A ring of miniature muqarnas faulting marks the zone of transition between the drum and dome.

Unlike the Mir-i Arab madrasa on the opposite side of the square, the mosque is an inward-facing building with no exterior windows. Even so, the inner courtyard is anything but claustrophobic. The arcaded walls are low enough that neighboring buildings are readily visible. As it is set on-axis with the Mir-i Arab madrasa, the domes of the madrasa rise over the east arcade, creating a sense of harmonious depth that draws the eye outward and upward. The graceful form of the closer–and far taller–Kalyan minaret accentuates this effect. By contrast, the interior of the courtyard is completely barren apart from a small octagonal kiosk on the west end and a solitary tree facing it to the east.

At present, the mosque remains in active use. Its continuous presence—in one incarnation or the other—underscores Bukhara’s status as one of the premiere Islamic cities of central Asia.