Driven by Thailand’s Bio-Circular Green Economy strategy, this study explores industrial waste utilization as a solution to mitigate the impacts of climate change and economic insecurity. This study involved interviews with farmers and field sampling across 131 sugarcane plantations, primarily in four districts in Kanchanaburi, western Thailand. The investigation aimed to assess heavy metal levels (As, Fe, Mn, Zn, Cu, Cr, Pb, Cd, Hg) in the plantation soils and their accumulations in soils and biomass under various agricultural practices, including the uses of filter cake and vinasse (industrial wastes from sugar–ethanol industries). Spatial analysis showed that As often exceeded national soil-quality standards for agriculture (25 mg kg−1). The Cd, As, and Zn tended to accumulate at a high level in most soils, whereas Pb accumulated locally. Factors such as clay content, soil alkalinity (for As and Mn), soil organic matters (As, Mn, and Hg), and no/minimum tillage (Zn and Cd) promoted the metal accumulation. Factor analysis showed that natural geochemical processes govern the spatial variations of the metals. The application of filter cake led to soils with elevated Cr, Fe, As, Cd, and Mn content and a clayey organic-rich composition, while the vinasse resulted in soils with higher levels of Zn, Cu, Fe, and clayey saline. The bioconcentration factors (BCF) revealed that sugarcane generally accumulated Hg (BCF ~2.32−35.72), whereas Cu (2.67) and As (1.04) tended to accumulate in sandy-soil farmlands. The waste utilization, however, neither contributed significantly to the concern levels of soil metals nor enhanced the bioconcentration of the soil metals into the sugarcane biomass. Utilizing the waste as fertilizer could benefit cane yield, but further studies should focus on proper fertilization rates and food safety.