The emergence, spread and intensification of agriculture, the impact of early agriculture on the natural environment and the possible role of climate on subsistence economies and population dynamics are important research questions in Japanese geoarchaeology. New directly dated archaeobotanical records of the Middle Yayoi (390–200 cal BCE, 1σ error) and Early Kofun (210–330 cal CE) periods from the Ikegami archaeological site and a 1300-year palynological record from the nearby Morinji Marsh help address these questions in the Kanto Plain of Central Japan. The pollen record suggests that management of chestnut and horse-chestnut by Final Jomon people in the study region declined around 750 cal BCE. The microcharcoal record indicates that human-induced fire activity decreased after 990 cal BCE and reached a minimum 500 years later, which coincides with the hemispheric-scale Iron Age Cold Epoch and late Bond event 2. Increasing use of fire from ca. 500 cal BCE is contemporaneous with the earliest evidence of millet-rice cultivation from south-western Kanto and the Central Highlands. This and pollen-based indicators of crop cultivation around Morinji Marsh ca. 200 cal BCE are consistent with the 14C-dated arrival of the first full-scale rice farmers at Ikegami. Their food economy still had a noticeable wild plant component (e.g. beans, walnut, horse-chestnut and acorn), however, the archaeobotanical assemblages from the Early Kofun period show a higher focus on rice cultivation and no evidence of a wild plant component. Variations in the charcoal concentrations and archaeobotanical data from the study region help postulate three phases of farming intensification related to cultural diffusion and/or migration. These phases, dated to ca. 500–300, 300–100 cal BCE and 100 cal BCE–250 cal CE, correspond to the pottery typologically defined late Early–early Middle Yayoi, middle–late Middle Yayoi and Late Yayoi periods, respectively.