The pharaohs of the first Egyptian royal Dynasty (c. 3000-2800 B.C.) chose to be buried at Abydos in Upper Egypt. Their courtiers, however, started a cemetery of massive rectangular tombs (known as mastabas) on the northern tip of the Saqqara plateau. From the Second Dynasty onwards, royal tombs were constructed at Saqqara too. Not much is known of these simple subterranean galleries. Although the last king of this line, Khasekhemuy, was again buried in Abydos, he also constructed a huge rectangular enclosure at Saqqara. This so-called Gisr el-Mudir set the example for his successor Djoser of the Third Dynasty (c. 2630-2611 B.C.), whose funerary complex comprises a similar enclosure of 545x277 m. Its centre is occupied by a dazzling architectural innovation: a 63 m high Step Pyramid, made by piling up six mastabas on top of each other. The rest of Djoser's enclosure contains a number of temples and dummy buildings, all built in bright white Tura limestone.

After Djoser, step pyramids soon developed into proper pyramids. At the same time, the enclosures became much smaller and merely enveloped a pyramid temple, joined to a valley temple at the edge of the cultivation by means of a sloping causeway. Most kings selected other Memphite cemeteries for their pyramids: Giza and Abusir north of Saqqara, or Dahshur and Meidum to the south. Still, Saqqara boasts the remains of the step pyramid of Sekhemkhet (Third Dynasty), the mastaba tomb of Shepseskaf (Fourth Dynasty, 2472-2467 B.C.), and the proper pyramids of Userkaf, Djedkarê, and Unas (Fifth Dynasty, 2465-2323 B.C.),and all the kings of the Sixth Dynasty (Teti, Pepi I, Merenrê, Pepi II, 2323-2150 B.C.). The five last monuments contain copies of the oldest religious texts from Ancient Egypt, the so-called Pyramid Texts.

By the time of Pepi II, many areas of the Saqqara plateau were already lined with mastaba tombs of Memphite courtiers and officials. Usually these rectangular structures comprise a number of offering chapels with wall decoration in limestone reliefs. Thus, Saqqara still forms a large open-air museum of Old Kingdom art. During the Middle Kingdom (2040-1640 B.C.) and New Kingdom (1550-1070) both the capital and the major cemeteries moved further south, and only two more mudbrick pyramids were built at Saqqara in the 13th dynasty. One of them was constructed by Khendjer, the other owner is unknown. Large-scale construction at Saqqara was not resumed until the middle of the Eighteenth Dynasty (from about 1400 B.C. onwards), when the pharaohs again devoted more attention to Memphis. Numerous high officials, priests, and artisans built their tombs in several clusters dispersed all over the plateau. These tombs were of a new type: a free-standing offering chapel or funerary temple, sometimes with open courtyard and pylon gateway, with rock-cut burial chambers deep underground. There were also some completely rock-cut tombs along the edge of the Saqqara escarpment. This period of use lasted for about two centuries, when the attention shifted again to the new capitals in the Nile Delta. During the last millennium B.C. a great number of shaft tombs was cut, until the whole substructure of the desert was honeycombed.

The same period witnessed great religious activity on the Saqqara plateau. The site developed into a place of pilgrimage, centred around the burial place of the sacred Apis bulls of Memphis (the Serapeum). The latter consists of vast underground galleries lined with the burial chambers for the individual bulls. Similar galleries were cut for other animal cults (cows, baboons, cats, dogs, ibises and hawks). This upsurge of the traditional Egyptian cults was followed by Christianity, which brought several monastic communities to the desert of Saqqara. After about 850 A.D., the plateau became utterly deserted and most of its monuments were gradually covered by drift sand.