The architecture of the Ayyubids and Atabeg Zangids incorporates a number of transitional features that connect it to late Fatimid and early Mamluk architecture, and therefore provides a level of continuity with both traditions.

In terms of building materials, stone is widely used in these architectural traditions since it is commonly available in the regions under Zangid and Ayyubid rule, Greater Syria and Egypt, and these architectural traditions do in fact provide some very high-quality stonework. Brick and stucco are more common in eastern Syria.

The arrangement to reconcile the different directions of the street and the qibla developed during the late Fatimid period becomes more commonplace during the Ayyubid period. Moreover, the broken-axis plan, developed earlier in the Fatimid Aqmar Mosque and used to connect the street to the interior of the structure in order to achieve the transition between the two directions, becomes more intricate.

A variety of minaret shapes appear during this period. Some consist of a square section, others of a circular one, while others feature a combination of a square section at the lower part of the shaft, and an octagonal or circular one at the top.

The use of the muqarnas is commonplace during the period, especially for vaulting, and features some of the earliest surviving examples of stone muqarnas compositions. Also, the use of the ablaq technique for facades (rows of stone in alternating colours) appears towards the end of the Ayyubid period. The technique is later used extensively by the Mamluks.

The Ayyubids left an impressive tradition of military architecture, built primarily in response to their struggle with the Crusaders. In fact, a number of fortresses built originally by the Crusaders were later taken over by the Ayyubids, who carried out considerable renovation and expansion on them. The fortresses of the Ayyubids were larger than those of preceding periods and they had thicker walls. They included features such as double and bent entrances, arrow slits that reached to the floor, the use of machicoulis, and gates decorated with talismanic figures such as snakes, dragons and lions. Another important development of the Ayyubid period is that the rulers of the time placed their residential palaces inside their citadels.

The madrasa emerged as an important component of the architectural heritage of the Zangids and Ayyubids. In fact, one of the earliest surviving examples of a madrasa anywhere in the Islamic world is a Zangid monument. The development of the madrasa was closely connected to supporting the teaching of Sunni Islam, in which the Zangids and Ayyubids were actively engaged. In plan, Ayyubid madrasas generally consist of a courtyard surrounded by two to four iwans (a vaulted space that is walled on three sides and open to a courtyard on the fourth), as well as smaller cells consisting of living units for the madrasa's students and teachers. With time, the four-iwan plan became predominant. The Ayyubids also introduced a combination of mausoleum and madrasa towards the end of their rule. This combination was used extensively by the Mamluks after them.