Natural substrates used in horticultural practice quickly degrade during plant cultivation. Methods to extend their service life are sought using natural materials, the acquisition and disposal of which do not burden the natural environment. The paper presents a sustainable method for modifying the coconut fiber substrate by impregnation with a wood-based isolate activated for polymerization and the addition of biochar pellets with retention-increasing properties. The modifications applied to the substrates were shown to have an impact on some of their physical properties, which directly impacted their usefulness in the horticultural production of dessert raspberries. It was found that after a year of operation, the modified substrates showed significantly lower levels of degradation markers. The shrinkage of the impregnated substrate was ~50% lower than that of the control sample, while the substrate with the addition of biochar pellets resulted in similar shrinkage and the lowest plant root mass (25.47%). The usefulness of these substrates was also verified by measuring the physiological parameters of the plants, which determined the ability to photosynthesize and build biomass, as well as susceptibility to stress potentially caused by substrate modifications. The recorded values of these parameters indicate, in most cases, that there is no disturbance of the homeostasis of raspberry plants grown using these substrates. However, plant productivity (measured by the yield of harvested raspberry fruit) indicates that the use of impregnated coconut fiber substrate with the addition of biochar pellets allows for obtaining the highest fruit yields (fruit yield—2.43 kg plant−1). The yields obtained in combination with the extended durability of the modified substrates during operation recommend this solution for use in horticultural practice and make the production more sustainable.