The European Food Safety Authority (EFSA) carried out a public consultation to receive input from the scientific community and all interested parties on the draft Guidance to develop specific protection goals options for environmental risk assessment at EFSA, in relation to biodiversity and ecosystem services. This Guidance presents a framework, which accounts for biodiversity and ecosystem services, to make general protection goals operational for use in all areas of EFSA’s Environmental Risk Assessments. The approach to follow has three sequential steps: (1) the identification of relevant ecosystem services; (2) the identification of service-providing units (SPUs) for these ecosystem services; and (3) the specification of options for the level/parameters of protection of the SPUs using five interrelated dimensions (ecological entity, attribute, magnitude of effects, temporal scale and spatial scale). This Guidance was prepared by a dedicated working group of the EFSA Scientific Committee and endorsed by the Scientific Committee for public consultation at its plenary meeting of 9 June 2015. The consultation was carried out via the web from 22 June 2015 and the draft guidance was published online with an invitation for submission of written comments by 10 September 2015. EFSA received 175 comments from 16 interested parties. The current report presents statistics on the comments received and lists all comments together with detailed answers to them. The submitted comments were considered valuable and were taken into account by the working group when updating the draft guidance. EFSA and its Scientific Committee wish to thank all stakeholders for their contributions. The finalised guidance was discussed and adopted at the Scientific Committee plenary meeting of 21 April 2016, and is published in the EFSA Journal.