The Minabe-Tanabe Ume System in central Japan is defined as a Globally Important Agricultural Heritage System (GIAHS) by the United Nations Food and Agriculture Organization. This study examined relationships between parcel-level plant diversity and land use, management, and development in traditional sloped Ume (Japanese apricot; Prunus mume) orchards and adjoining level orchards recently developed through large-scale cut-fill land development. We constructed and overlaid past (1974) and present (2015) digital land-use maps to assess land use and topography. We conducted field vegetation surveys in land parcels with different development and management histories. Although 249 ha (4.6% of the total 2015 area) were developed using cut-fill methods, 5148 ha remain a traditional orchard surrounded by coppice forests. Vegetation surveys and a two-way indicator species analysis revealed that traditional orchards had more native species and a higher plant diversity index. Cut-fill orchards contained a higher proportion of alien species; however, the degree depended on parcel history and management. Overall, this area remains a dynamic mosaic landscape containing a core of long-standing Ume orchards. We suggest that biodiversity conservation in this area should focus on conservation measures such as indirect land-use regulations, including some acceptable landform transformations, to promote continued farming of this ecologically important area.