Djoser’s mortuary complex comprises the great trench, enclosure wall, colonnaded entrance, ‘T’ temple, Sed festival complex, north and south pavillons, south tomb and court, western mounds, mortuary temple, and the crowning feature of it all, the step pyramid with its substructure. The complex was a landmark achievement for Egyptian architecture. It was the advent of the pyramidal form of the royal tomb and the first instance of the mass use of limestone in construction, replacing mudbrick which had been the staple building material prior. This shift to limestone – a hard, dense material compared to mudbrick – presented novel challenges to the architects. Though they kept to earlier tradition, copying architectonic elements and carving them into the stone. For example, the Egyptians hand-carved 1,680 9 m (30 ft; 17 cu) tall niches out of the limestone enclosure wall.  In earlier projects, this element was built with wooden planks, ropes, and poles hung with reed mats. In a modern context, the same element would be built by laying out the blocks to form the recesses.

Complex layout: 1) step pyramid, 2) south tomb and chapel, 3) Sed festival complex, 4) ‘T’ temple, 5) south court, 6) south pavillon, 7) north pavillon, 8) mortuary temple, 9) western mounds, 10) colonnaded entrance, 11) north court, 12) north galleries, 13) step tombs, 14) serdab, and 15) north altar

The crowning feature of the complex is the Step Pyramid which rises from the Saqqara plateau in six steps to a height between 60 m (200 ft; 110 cu) and 62.5 m (205 ft; 119.3 cu). This element was revised repeatedly in construction, going through a series of developmental phases that culminated in its step pyramidal form. These phases are traditionally labelled, following Jean-Philippe Lauer’s excavations: M1, M2, M3, P1, P1′, and P2.

In the early stages (M1 to M3) the structure had the form of a mastaba before alterations (P1 to P2) were made to create its step pyramidal form. In the first stage (M1), the mastaba had a square plan 63 m (207 ft; 120 cu) in length that rose to a height of 8.4 m (28 ft; 16 cu). This was built from a core of limestone blocks arranged in horizontal beds and bound with yellow or red clay. A 2.6 m (9 ft; 5 cu) thick casing of fine white Tura limestone was applied to the core arranged in the same horizontal manner. The outer blocks were inclined to ~82° and the top of the mastaba likely had a slightly convex shape. A second casing of fine white limestone was applied to this which increased the mastaba’s base length to 71.5 m (235 ft; 136 cu) square (M2). The casing was 4.2 m (14 ft; 8 cu) thick at the base and 3.4 m (11 ft; 6.5 cu) thick at the peak, which was 0.65 m (2 ft; 1 cu) lower than the initial mastaba height. The outer blocks of this second coat also had a steeper incline at ~76°. The mastaba was then extended 8.4 m (28 ft; 16 cu) east to cover a series of eleven shafts 33 m (108 ft; 63 cu) deep that ended in passages that led west to the burial chambers of members of Djoser’s family. This extension was built from locally sourced limestone rubble and cased by 1.5 m (5 ft; 3 cu) thick limestone coating that formed an extension of M2. The mastaba had a new, rectangular ground plan 71.5 m (235 ft; 136 cu) by 79.5 m (261 ft; 152 cu). At this stage the mastaba still peaked at 8.4 m (28 ft; 16 cu) in height, too short to be seen from outside the 10.5 m (34 ft; 20 cu) high enclosure wall.

Egyptologists are split on the motivations behind the conception of the pyramidal form that the mastaba was converted into. Lauer believed that the alteration was made to have the tomb visible from Memphis. The fact of the mastabas square plan led Rainer Stadelmann, however, to suggest that it was never the intended final form and that it was planned to be a pyramid from the outset. The conversion (P1) encased the mastaba (M3) extending its length by 5.76 m (19 ft; 11 cu) on each axis giving it a base length of 85.5 m (281 ft; 163 cu) by 77 m (253 ft; 147 cu). The alteration from mastaba to pyramid came with a shift in construction. The builders used larger and better quality, roughly dressed limestone blocks – but instead of horizontal beds, they built successive inclined accretion layers 2–3 m (6.6–9.8 ft) thick. These leaned on each other from opposite ends providing greater stability preventing a collapse. The whole was then cased in fine white limestone with a layer of packing in between. This phase of the pyramid had four steps that rose to a height of 42 m (138 ft; 80 cu). The decision was then made to expand the pyramid north and west from four to six steps (P1′) which was then finished with a final layer of limestone casing (P2) that gave the pyramid its final form. On completion the step pyramid had a base length of 109 m (358 ft; 208 cu) by 121 m (397 ft; 231 cu) that rose to a height of 60–62.5 m (197–205 ft; 115–119 cu) and occupied a volume of 330,400 m³ (11,670,000 cu ft).

Much of the rock for the pyramid was likely quarried from the construction of the great trench. It is widely accepted that ramps would have been used to raise heavy stone to construct the pyramid, and many plausible models have been suggested. For transport, apparatuses like rollers were used in which the heavy stone could be placed and then rolled.

Under the step pyramid is a labyrinth of tunneled chambers and galleries that total nearly 6 km in length and connect to a central shaft 7 m square and 28 m deep. These spaces provide room for the king’s burial, the burial of family members, and the storage of goods and offerings. The entrance to the 28 m shaft was built on the north side of the pyramid, a trend that would remain throughout the Old Kingdom. The sides of the underground passages are limestone inlaid with blue faience tile to replicate reed matting. These “palace façade” walls are further decorated by panels decorated in low relief that show the king participating in the Heb-sed. Together these chambers constitute the funerary apartment that mimicked the palace and would serve as the living place of the royal ka. On the east side of the pyramid, eleven shafts 32 m deep were constructed and annexed to horizontal tunnels for royal family members. These were incorporated into the pre-existing substructure as it expanded eastward. In the storerooms along here over 40,000 stone vessels were found, many of which predate Djoser. These would have served Djoser’s visceral needs in the afterlife. An extensive network of underground galleries was located to the north, west and south of the central burial chamber and crude horizontal magazines were carved into these.