Abstract The European Food Safety Authority (EFSA) requested the Panel on Plant Health to develop a methodology for assessing the environmental risks posed by harmful organisms that may enter, establish and spread in the European Union. To do so, the Panel first reviewed the methods for assessing the environmental risks of plant pests that have previously been used in pest risk assessment. The limitations identified by the review led the Panel to define the new methodology for environmental risk assessment which is described in this guidance document. The guidance is primarily addressed to the EFSA PLH Panel and has been conceived as an enhancement of the relevant parts of the “Guidance on a harmonised framework for pest risk assessment and the identification and evaluation of pest risk management options by EFSA”. Emphasizing the importance of assessing the consequences on both the structural (biodiversity) and the functional (ecosystem services) aspects of the environment, this new approach includes methods for assessing both aspects for the first time in a pest risk assessment scheme. A list of questions has been developed for the assessor to evaluate the consequences for structural biodiversity and for ecosystem services in the current area of invasion and in the risk assessment area. To ensure the consistency and transparency of the assessment, a rating system has also been developed based on a probabilistic approach with an evaluation of the degree of uncertainty. Finally, an overview of the available risk reduction options for pests in natural environments is presented, minimum data requirements are described, and a glossary to support the common understanding of the principles of this opinion is provided.