The increasing amount of bio-waste creates the need to develop a method for efficient management based on processes that are more environmentally friendly than incineration and composting. This research aimed to utilize the waste of raspberry seeds after supercritical CO2 extraction. The biomass was enriched with micronutrients by the biosorption process to prepare micronutrient fertilizers for organic farming and biofortification of raspberries fruits. It was observed that at 100% dose of micronutrients, raspberry crop yield increased by 3%, and transfer of micronutrients to fruit biomass increased by 4.7%, 6.4%, and 8.8% (Cu, Mn, Zn, respectively) compared to commercial fertilizer. The supply of micronutrients at a dose of 150% led to a significant increase in micronutrient content of 3%, 41%, and 8% (Cu, Mn, and Zn, respectively) compared to commercial fertilizer. Research shows that the application of higher doses of micronutrients leads to the enrichment of edible parts of fruits, and fertilizers ensure environmental safety. The fruits contained on average 11.5% more microelements compared to the groups fertilized with the commercial product. The fruit yield (9.09-10.4 Mg per hectare) and the sugar content (9.82-10.2%) were also the highest. The micronutrients released from fertilizers and available to plants throughout the vegetation period affect the increase in yield, especially in the case of plants fruiting several times a year.