The south end of the courtyard is framed by the portico of the mosque. Surmounted by seven domes, each six meters in diameter, the portico of the mosque contains larger bays than the enclosure portico. These seven domes are carried by eight columns on the north, and rest on octagonal drums. Just behind the portico, the dominating single dome of the mosque rises thirty-five meters above the ground. Spanning twenty meters, the dome is carried over an almost skeletal system composed of four "elephant feet" (massive piers) and the arches between them. These polygonal piers, mostly projected on the façade for creation of a more spacious interior, rise to the level of the drum and increase the total mass available to support the load of the dome. An innovative design, this addition of these structural piers allows for a shift from purely load-bearing to thinner, heavily fenestrated walls. Thus, all four tympana feature three rows of windows with seven arched windows at the bottom, five arched and two circular windows in the middle, and three arched and two circular windows at the top. The dome itself also features twenty-four windows, greatly increasing the quantity of natural light within the interior; the total number of windows in the prayer hall is close to two hundred. Along the east-west axis of the prayer hall, the mosque has side bays, each of which are topped by three domes. Measuring six meters in diameter, these domes sit on columns with carved stalactite capitals. The height of these side bays is almost half that of the central space, and they include three rows of windows, the same number found in the large tympana of the main dome. The mosque has a slim minaret with a single balcony constructed of stone that corresponds to the western bay of the portico. 

Below the platform of the mosque-madrasa building (to the southeast) lies a large enclosure occupying a rectangular space used as a cemetery. At its western end is an L-shaped building that serves as the burial place of Güzelce Ahmed Paşa, the son-in-law of Mihrimah Sultan and vizier to sultan Selim II. The long arm of the L has three bays: a central domed bay and two smaller, rectangular bays flanking it to the north and south. The short arm has two rooms: one with a small dome.

The baths and fountain are located to the southeast of the complex, across a lane. These suffered significant neglect and were used as storage areas at one point.