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The choice of method for aggregation of ecological indicators is important for the outcome of the aggregation. We demonstrate and discuss how additive versus risk of system failure (i.e. use of one-out-all-out logic) aggregation methods can result in opposing outcomes when assessing the conservation status of habitat types under the EU-habitat directive. In additive aggregation systems, failure to meet a given ecological indicator that is required for favorable conservation status can be compensated by other indicators. The consequence is that ecosystem changes that are detrimental in the long term may be ignored when an additive aggregation method is applied. Despite this, additive aggregation systems appear to be dominant among conservationists and are frequently used to assess habitat status. We recommend the risk of system failure method when developing habitat quality assessment systems instead of only relying on additive aggregation systems.