Archaeological excavation has indicated that around 2600 BC, timber was abandoned in favour of stone, and two concentric arrays of holes (the Q and R Holes) were dug in the centre of the site. These stone sockets are only partly known (hence on present evidence are sometimes described as forming ‘crescents’), however they could be the remains of a double ring. Again, there is little firm dating evidence for this phase. The holes held up to 80 standing stones (shown blue on the plan) only 43 of which can be traced today. The bluestones (some of which are made of dolerite, an igneous rock), were thought for much of the 20th century to have been transported by humans from the Preseli Hills, 250 kilometres (160 mi) away in modern day Pembrokeshire in Wales. A newer theory is that they were brought from glacial deposits much nearer the site, which had been carried down from the northern side of the Preselis to southern England by the Irish Sea Glacier. Other standing stones may well have been small sarsens, used later as lintels. The stones, which weighed about four tons, consisted mostly of spotted Ordovician dolerite but included examples of rhyolite, tuff and volcanic and calcareous ash; in total around 20 different rock types are represented. Each monolith measures around 2 metres (6.6 ft) in height, between 1 m and 1.5 m (3.3-4.9 ft) wide and around 0.8 metres (2.6 ft) thick. What was to become known as the Altar Stone (1), is almost certainly derived from either Carmarthenshire or the Brecon Beacons and may have stood as a single large monolith.

The north eastern entrance was also widened at this time with the result that it precisely matched the direction of the midsummer sunrise and midwinter sunset of the period. This phase of the monument was abandoned unfinished however, the small standing stones were apparently removed and the Q and R holes purposefully backfilled. Even so, the monument appears to have eclipsed the site at Avebury in importance towards the end of this phase.

The Heelstone, a Tertiary sandstone, may also have been erected outside the north eastern entrance during this period although it cannot be securely dated and may have been installed at any time in phase 3. At first, a second stone, now no longer visible, joined it. Two, or possibly three, large portal stones were set up just inside the north eastern entrance of which only one, the fallen Slaughter Stone (4), 4.9 metres (16 ft) long, now remains. Other features loosely dated to phase 3 include the four Station Stones (6), two of which stood atop mounds (2 and 3). The mounds are known as ‘barrows’ although they do not contain burials. The Avenue, (10), a parallel pair of ditches and banks leading 3 kilometres (1.9 mi) to the River Avon was also added. Two ditches similar to Heelstone Ditch circling the Heelstone, which was by then reduced to a single monolith, were later dug around the Station Stones.