The recovery of plant mineral nutrients from the bio-based value chains is essential for a sustainable, circular bioeconomy, wherein resources are (re)used sustainably. The widest used approach is to recover plant nutrients on the last stage of biomass utilization processes-e.g., from ash, wastewater, or anaerobic digestate. The best approach is to recover mineral nutrients from the initial stages of biomass biorefinery, especially during biomass pre-treatments. Our paper aims to evaluate the nutrient recovery solutions from a trans-sectorial perspective, including biomass processing and the agricultural use of recovered nutrients. Several solutions integrated with the biomass pre-treatment stage, such as leaching/bioleaching, recovery from pre-treatment neoteric solvents, ionic liquids (ILs), and deep eutectic solvents (DESs) or integrated with hydrothermal treatments are discussed. Reducing mineral contents on silicon, phosphorus, and nitrogen biomass before the core biorefinery processes improves processability and yield and reduces corrosion and fouling effects. The recovered minerals are used as bio-based fertilizers or as silica-based plant biostimulants, with economic and environmental benefits.