The PII period dates from about A.D. 900 to 1100. During this time over most of the Pueblo world, villages are relatively small and dispersed widely across the landscape. A very common form of settlement is the "unit pueblo," consisting of a limited number of masonry rooms placed end-to-end in a linear block or L-shaped arrangment, with a small subterranean structure (interpreted as a kiva) a few meters away from the rooms. Although this is the general pattern of residence during PII, it is also the time of the so-called "Chaco phenomenon," involving the construction of Great Houses and Great Kivas. The system was centered in Chaco Canyon, with outlying Great Houses and Great Kivas ("Chaco outliers") connected with the canyon via an elaborate and massive road system. However, it should be remembered that not all Anasazi people were connected with the Chaco system (especially the Virgin Branch and Kayenta Anasazi, living to the north and west of the Chaco system, and the Rio Grande area, to the east), and even within the area encompassed by Chaco, most people lived in very small and "typical" PII settlements.

There is further elaboration of black-on-white, black-on-red, and gray ware pottery. Toward the end of PII, the first "polychrome" ceramics appear, painted in red, orange, and black designs. Black-on-white ceramic styles are very widespread and generally similar across vast areas, with some minor local variation. During PII, there is evolution of the gray ware "corrugated" pottery. Early in PII, the common form of corrugation is neck banding, similar to the style of PI. However, through time the neck bands become smaller and more elaborate, with the corrugations often finely pinched with the fingers to make small, scalloped designs. In middle to late PII, the pottery becomes corrugated all over, sometimes with very deeply and finely pinched corrugations. After the mid-1000s, many of the black-on-white and black-on-red pottery styles across a broad area of the northern Southwest show some influence from designs originating from Chaco Canyon.

In PII, there is a great deal of architectural standardization across very large regions. This is reflected in the "unit pueblo" form, but also in the ways in which individual rooms and other architectural features were built.

One puzzling aspect of PII is the general absence of large, subterranean structures (great kivas) in many areas. This is especially true for the Kayenta Anasazi. The dispersed settlement pattern therefore seems to be correlated with a lack of inter-village integration, implying considerable autonomy of individual settlements. The wide dispersal of small sites across the landscape implies that people did not feel especially threatened by their neighbors and were not compelled to aggregate for defensive reasons.

In some areas during PII, there appears a new architectural form, the "field house," consisting of a small room or set of rooms occupied on a daily basis or on a seasonal basis. These field houses are thought to be small structures placed out in the agricultural fields, used by people tending the fields.

Social organization during PII is not well understood, particularly with repsect to the Chaco system. Was Chaco a mighty empire with the ability to coerce and control outlying populations, or was it a great religious and ceremonial system that was a place of pilgrimage? The debate has convincing arguments on both sides. David Wilcox has argued in various publications that the Chacoans were able to send out relatively small but well-trained and fearsome groups of armed men to control outlying populations and demand "tribute" (gifts of food and other valuable items) for consumption or use by elites living in the Canyon Great Houses and in the outlying Great Houses. Others (Steve Lekson, John Stein) have argued that Chaco may have been a great ceremonial/religious center, where pilgrims came to participate in feasting and ceremonies. It is interesting to note that some of the features of Chaco Canyon (arc-shaped room blocks, great kivas, evidence for mass consumption of food) were also present in PI sites (see above). Was the Chaco system then the driving intellectual, philosophical, and religious force of the 900s through early 1100s, or did it merely reflect and reinforce ancient concepts and principles of the Anasazi?