Cycles of demographic and organizational change are well documented in Neolithic societies, but the social and ecological processes underlying them are debated. Such periodicities are implicit in the “Pecos classification,” a chronology for the pre-Hispanic U.S. Southwest introduced in Science in 1927 which is still widely used. To understand these periodicities, we analyzed 29,311 archaeological tree-ring dates from A.D. 500 to 1400 in the context of a novel high spatial resolution, annual reconstruction of the maize dry-farming niche for this same period. We argue that each of the Pecos periods initially incorporates an “exploration” phase, followed by a phase of “exploitation” of niches that are simultaneously ecological, cultural, and organizational. Exploitation phases characterized by demographic expansion and aggregation ended with climatically driven downturns in agricultural favorability, undermining important bases for social consensus. Exploration phases were times of socio-ecological niche discovery and development.