Early decisions in the technology development phase can represent large impacts on its future environmental performance. It has been estimated that around 80% of the total environmental impacts are associated to the design phase. However, emerging technologies at low TRL (2-5) have limited amount of data, scale up issues and uncertainties, which make challenging carry out a standard LCA. This work introduces an LCA-based methodology with an eco-design approach by identifying environmental hotspots and extending the analysis with an iterative sensitivity analysis of the associated parameters. This approach is dedicated to emerging technologies with low TRL to evaluates the how processes and design parameters can improve its environmental footprint. A case study of an emerging technology based on an innovative rotating biofilm for microalgae production (algae meal) at low TRL is presented to illustrate this methodology. The inventory data are based on an industrial production pilot and biomass conversion system developed by the small sized enterprise Inalve S.A. (Nice, France). For the first stage, a preliminary process design is based on pilot data, these data are complemented by literature information for the technologies not yet implemented at pilot scale. The second stage is based on the process modelling outputs (inventory data). The potential environmental impacts are evaluated through two life cycle impact methods, EF and CED. Based on the environmental impacts, the relevant process steps were identified, i.e., process steps with contributions higher than 10% of the total impact in each impact category evaluated. The relevant parameters for the hotspots process steps were then identified and evaluated in a sensitivity analysis. The eco-design parameters influence the process design inventory and the environmental impacts. Thus, this methodology is iterative, i.e., for each eco-design parameter, the process modelling was updated, and the LCA impacts were re-evaluated. In addition, the overall environmental impacts are evaluated for different functional units and this eco-designed technology was compared with classical approached for producing aquafeed 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 (lifespan and composition) and electricity consumption (power rotor and blower) turned out to be the crucial eco-design parameters. Impact reduction ranging from 25% to 88.3% were obtained by eco-designing this new technology. Environmental footprint of algae meal from rotating algal biofilms outperformed the other scenarios by at least 70.8%. This methodology leads to the identification and optimization of the main eco-design parameters. It can guide technology developers of emerging technologies to better understand the implications of design choices on the future environmental impacts and optimize the eco-design. Due to the economic allocation for the products and co-products, without market yet, the evaluated impacts remain highly sensitive to the economic price of these products. The trickiest step in the extrapolation phase is therefore to assess a realistic future market price for these non-conventional feeds and their co-products, at a stage where they are not produced. The assumptions on the process economics must therefore be later updated to consolidate the impact analysis.