Global agro-biodiversity has resulted from processes of plant migration and agricultural adoption. Although critically affecting current diversity, crop diffusion from antiquity to the middle-ages is poorly researched, overshadowed by studies on that of prehistoric periods. A new archaeobotanical dataset from three Negev Highland desert sites demonstrates the first millennium CE's significance for long-term agricultural change in southwest Asia. This enables evaluation of the "Islamic Green Revolution" (IGR) thesis compared to "Roman Agricultural Diffusion" (RAD), and both versus crop diffusion since the Neolithic. Among the finds, some of the earliest Solanum melongena seeds in the Levant represent the proposed IGR. Several other identified economic plants, including two unprecedented in Levantine archaeobotany (Ziziphus jujuba, Lupinus albus), implicate RAD as the greater force for crop migrations. Altogether the evidence supports a gradualist model for Holocene-wide crop diffusion, within which the first millennium CE contributed more to global agro-diversity than any earlier period.