Despite decades of lively debate about Taiwan’s role in the spread of early agriculture, crops and cultivation practices to the Indo-Pacific region, there is little archaeobotanical data from the island. Here we present the first directly dated and systematically analysed macrobotanical records from Taiwan obtained by flotation at the archaeological site Sanbaopi 5 (23°07′03′′N, 120°15′32′′E), representing the Dahu (1400 BCE–100 CE) and Niaosong (100–1400 CE) culture periods. The results suggest that Middle Dahu (900–100 BCE) communities in the study area practiced rainfed crop cultivation with mainly foxtail (Setaria italica) and broomcorn (Panicum miliaceum) millet and rice (Oryza sativa). Pulses (Vigna angularis, Glycine soja/max) were also part of the subsistence of local farmers and used as supplementary food and/or green manure. The archaeobotanical record together with archaeological site data for prehistoric China substantiates evidence that the Dahu culture originates in the Lower Yellow River region and migrated to Taiwan along the East China Sea coast. The emergence of the Dahu culture coincided with the spread of mixed millet-rice farming to the Korean Peninsula and Japan and was possibly related to enhanced economic and political expansion of the Shang and Western Zhou dynasties and the long-term weakening of summer monsoon precipitation. Pigeon pea (Cajanus cajan) and mung bean (V. radiata var. radiata) assemblages from the sixth century CE Niaosong period highlight the influx of goods, crops, knowledge and people from South and Southeast Asia via southern routes in the context of enhanced exchange across the South China Sea region.