The increasing demand for Rare Earth Elements (REEs) and the depletion of mineral resources motivate sustainable strategies for REE recovery from alternative unconventional sources, such as REE hyperaccumulator. The greatest impediment to REE agromining is the difficulty in the separation of REEs and other elements from the harvested biomass (bio-ore). Here, we develop a sulfuric acid assisted ethanol fractionation method for processing D. linearis bio-ore to produce the pure REE compounds and value-added chemicals. The results show that 94.5% of REEs and 87.4% of Ca remained in the solid phase, and most of the impurities (Al, Fe, Mg, and Mn) transferred to the liquid phase. Density functional theory calculations show that the water-cation bonds of REEs and Ca cations were broken more easily than the bonds of the cations of key impurities, causing lower solubility of REEs and Ca compounds. Subsequent separation and purification led to a REE-oxide (REO) product with a purity of 97.1% and a final recovery of 88.9%. In addition, lignin and phenols were obtained during organosolv fractionation coupled with a fast pyrolysis process. This new approach opens up the possibility for simultaneous selective recovery of REEs and to produce value-added chemicals from REE bio-ore refining.