In this paper, we use preliminary archaeological data spanning the Iron Age through Medieval periods (ca. 800 BCE to 1200 CE) in the Juuku Valley on the south side of Lake Issyk-Kul to model land use across vertical mountain zones. We have (1) established a radiometric chronology; (2) conducted test excavations of an Iron Age settlement at 2100 m asl and a Turkic period burial at 1934 m asl; (3) undertaken preliminary archaeobotanical research; and (4) performed pedestrian surveys. Seed remains of wheat (Triticum aestivum), barley (Hordeum vulgare), broomcorn millet (Panicum milaceum) and foxtail millet (Setaria italica), and legumes were recovered in very small quantities from both sites. We compare these preliminary archaeobotanical results with previously published data from the Talgar Iron Age settlements on the north side of the Tian Shan Mountain range in Kazakhstan. A small assemblage of faunal remains found at the Turkic period kurgan and from a profile at the upland Iron Age settlement demonstrates the practice of herding sheep/goats, cattle, and horses in the Juuku Valley. The goal of this study was to test the hypothesis that pastoral transhumance and agropastoralism were interchangeable economic strategies used by peoples in the Iron Age through Medieval periods in mountain-river valleys between 600 m to 2100 m asl. These economic strategies combined the pasturing of sheep, goats, cattle, and horses with the cultivation of cereals were adapted to different vegetational zones along a vertical gradient. This paper is based on preliminary research of upland sites of the Juuku Valley in Kyrgyzstan, and initiates a long-term research study of four millennia of settlements that ranged from pastoral transhumance and combined mountain agriculture using survey data and test excavations.