Floating Offshore Wind Farms (FOWFs) are the most promising renewable energy resource. Floating turbines are installed at progressively increasing water depths, interacting with offshore and deep-sea ecosystems. Thus, specific criteria to enable a sound and accurate Environmental Impact Assessment (EIA) are required. The still limited understanding of the impacts of FOWFs, and the concerns for the conflicts in the use of maritime space (e.g., fisheries), might lead to a more precautionary approach and constrain their development. Here we describe the characteristics of the deep habitats potentially impacted and identify a set of comprehensive and standardized criteria, response variables and approaches for a reliable EIA based on an Ecosystem-based approach. These analyses will support an appropriate design and site prioritization to respect the “Do No Significant Harm" principle. Considering the wide heterogeneity among habitats and geographic regions, we examined the potential interactions of FOWFs with i) Vulnerable Marine Ecosystems; ii) critical habitats; iii) migratory routes of large marine vertebrates; iv) habitat-forming species, benthic/pelagic organisms, v) migratory routes of birds/chiropters; vi) other human uses leading to cumulative/synergistic effects and any other potential interference. We identified mitigation and compensation measures and explored the potential of wind-farm areas as “Other Effective Conservation Measures” to support sustainable fisheries and passive restoration. Adequate siting, EIA and systematic monitoring can minimize FOWFs’ environmental interactions, with final negligible, or even positive effects on marine ecosystems. Standardized criteria could significantly reduce the bottlenecks in permitting while offering a strategic vision for the sustainable use of the maritime space.