Microalgae are recognized as a high-nutritional quality non-conventional feed resource which can contribute to address the increasing food demand. This study focuses on a breakthrough microalgal production system, based on rotating biofilm, with the objective of assessing and reducing its environmental impact for two microalgae-based products: algal biomass and protein concentrate (algae meal). The methodology is based on Life Cycle Assessment (LCA) with an eco-design approach. This approach is dedicated to emerging technologies with low technology readiness level. Eco-design parameters were identified from the process modelling and its environmental assessment through an iterative sensitivity analysis. The results for algae meal were compared with soymeal and fishmeal and benchmarked with alternative production technologies. 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. Algae meal from eco-designed rotating biofilm has an environmental impact reduced by at least 70.8% in comparison to conventional aquafeeds (fishmeal and soymeal).