It has become clear how important it is to assess longer term effects of (nano) materials in the environment given the current evidence showing how epigenetics drives response mechanisms. Here we studied global DNA methylation in standard soil invertebrate Enchytraeus crypticus over 224 days when exposed to nanostructured tungsten carbide cobalt (WCCo nanomaterials (NMs)) and to cobalt (CoCl₂) in a multigenerational experiment. In order to assess the transgenerational effect, we used a multigenerational (MG) test design consisting of four generations in spiked soil followed by two generations in clean soil. Results showed that MG exposure to WCCo NMs caused global DNA methylation to increase, which continued in unexposed generations and was associated with an increase in reproduction (phenotypic effect). In general, WCCo NMs caused more (and more consistent) methylation than CoCl₂.