During the Late Horizon the reorganization that took place under Inka rule is evident in settlement pattern changes and ceramics distributions. At the Chivay obsidian source, the highest quantity of diagnostic ceramics were those in Late Horizon styles. These ceramics may be derived from the mortuary structures that were encountered in the Maymeja source area, or the LH ceramics may be a reflection of the increased investment in water control projects and expanded herding. A possible extension to the Huarancante canal capturing water from Quebrada de los Molinos would have had its origins precisely at the Maymeja workshop at the Chivay source.

Elsewhere in the survey area the Inka period introduced a number of changes including distinctive differences in long-distance interaction. In Block 2, the Late Horizon component appears to have been consolidated around a few larger sites. The presence of Titicaca Basin pottery is notably lower in the Late Horizon in Block 2, and Cusco Inka styles are introduced in that area. Fourteen sherds of Colla style pottery (Titicaca Basin LIP) were found in Block 2, and these were primarily scattered in the northern half of the block. By the subsequent Late Horizon only two Chucuito style sherds (Titicaca Basin LH) were found in Block 2. The most common decorated pottery was the local LH Collagua-Inka and the Collagua-3 style. In Block 3, settlement became concentrated at agricultural plots along natural river terraces near the confluence of the Río Colca and Río Llapa in an area known as Callalli Antiguo. A concentration of structures with non-local Inka pottery along the principal road system on the south side of the Colca suggests that this site may have had administrative functions in the Late Horizon settlement pattern.