Native and exotic earthworms and plants co-exist on the margins of agricultural land in New Zealand. Remnants of native vegetation support mixed assemblages of depleted populations of native Megascolecid earthworms together with apparently increasing invasive populations of introduced Lumbricidae. We question whether the survival and viability of these earthworm populations is a function of soil preference and whether there are significant differences in terms of how the two groups are influenced by and modify soil properties and plant growth. Choice chamber and mesocosm experiments, with and without plant rhizospheres, were used to study five species of native earthworms, two of which could be identified only by DNA barcoding, and four introduced exotic species. Both natives and exotics preferred agricultural soils to a plantation forest and a native forest soil. Earthworms also modified the physico-chemistry of soils and greenhouse gas emissions, with a marked interaction with root morphology of two native species of tea tree. Lesser differences were found between native and exotic earthworms than between functional groups. It is concluded that New Zealand’s production landscapes provide novel habitats with clear benefits both to threatened species conservation and to soil ecosystem services.