<p>This research aimed to develop a circular technology for producing micronutrient-rich (Cu(II), Fe(II), Mn(II), and Zn(II)) fertilizers for cucumber cultivation. The target micronutrient content of the fertilizers was set to exceed 1.5%. Various renewable resources and agricultural wastes were tested as potential raw materials. The final fertilizers were produced using blackcurrant seeds, blackcurrant residues, and flaxseed cake, which contain nitrogen and organic carbon concentrations greater than 3.0% and 45.0%, respectively. Conventional immersion biosorption and specially designed spraying biosorption methods were employed to enrich the biomass with micronutrients. The effectiveness of the fertilizers was assessed through cucumber germination tests, and the fertilizers were characterized based on their nutrient and pollutant content, particle/molecular structure, surface topography, and compliance with fertilizer product standards. The highest obtained total micronutrient content was 2.5%, with nitrogen levels ranging from 3.54 to 3.97% and carbon at 45%. The bioavailability of the micronutrients in the biomass was significantly higher compared to conventional fertilizers, showing 60–100% availability. The biofortified cucumbers produced using these micronutrient-enriched fertilizers present a sustainable solution to micronutrient malnutrition and offer a greener alternative to conventional fertilizers. These new fertilizers have the potential to contribute significantly to a more sustainable food and agriculture system.</p> Graphical Abstract (created in biorender.com) <p></p>