Appropriate choices in the early technology development phase of a process can avoid large impacts on its future environmental performance. LCA can support efficient eco-conception, driving the development of immature technologies by identifying environmental hotspots and proposing alternatives with reduced impact. This work introduces an LCA-based methodology with an eco-design approach that aims to quantitatively demonstrate the importance in the selection of design parameters on the environmental impacts. The overall environmental impacts are evaluated for different functional units, extending the analysis to identification of process hotpots with iterative sensitivity analysis of the associated parameters. A case study based on an innovative Rotating Algal Biofilm (RAB) technology for microalgae (algae meal) production is presented to illustrate this methodology. The eco-design parameters were spotted from the process modelling through an iterative analysis. The resulting eco-designed technology was compared with classical approaches for producing protein sources (soymeal and fishmeal), and with other microalgae cultivation technologies (ORP and rotating carpet biofilms). Results show that the NH3 emission factor, fabric support properties and electricity consumption turned out to be the crucial eco-design parameters. The impacts of the new eco-designed technology were reduced in a range from 25% to 88.3%. Algae meal from rotating algal biofilms outperformed the environmental footprint of the other conventional aquafeeds (fishmeal and soymeal). The proposed methodology can guide technology developers to understand the implications of design choices on the future environmental impacts. Since economic allocation was chosen, the evaluated impacts remain highly sensitive to the future price of these products.