Distributing fishing mortality across the widest possible range of species, stocks, and sizes in proportion to their natural productivity (i.e., balanced harvest, BH) has been suggested as a new paradigm of fisheries management to minimize the effects of fishing on the ecosystem structure while maximizing overall yield. Models that have been used to test the effects of BH, however, usually concentrate on fish and assume full alignment of fishing mortality with the productivity of each species. Here, we used the trophic-level-based approach EcoTroph to investigate the effects of BH on the biomass and catch trophic spectra of a virtual ecosystem assuming (1) a full implementation, where all trophic levels can be fished according to their productivity and (2) a more realistic implementation, where low and intermediate trophic levels are only partially exploitable by fisheries mimicking current technological and practical limitations. EcoTroph simulations show that a BH fishing pattern does not fully maintain ecosystem structure but results in small structural changes and a large total yield. The resulting catch, however, was dominated by low trophic levels (i.e., 2-2.5). Considering that fishing mortality cannot be fully aligned to all species, we observed an additional adverse impact of BH: the increase in unexploitable biomass. In contrast, protecting lower trophic levels appeared as an efficient way to limit the impact of fisheries on the highest trophic levels, which play a crucial role in ecosystem stability and biodiversity. We conclude that given our inability to align fishing mortality to the productivity of each species, BH could lead to strong adverse impacts on the ecosystem. Instead of expanding fishing pressure toward new species and trophic levels, we first should ensure the sustainable management of those that are currently harvested beyond their capacity to replenish.