Ecological Risk Assessment (ERA) of genetically modified crops for the soil environment is supported by guidelines already available for pesticides. They have very much in common and here we point out the salient features of empirical ERA methodology for soil invertebrates and the need to address ecosystem services through assessment of ecological processes contributed by soil invertebrate functional traits. The soil quality, bait lamina test, and earthworm burrowing activity are current candidates underpinning an ecosystem services assessment approach. Establishing functional trait databases, baseline data, and making links between them, will enable future assessment of soil ecosystem services.