Ecology Letters (2011) Assembly history, or the order of species arrival, can have wide‐ranging effects on species, communities and ecosystems. However, it remains unclear whether assembly history primarily affects individual species, with effects attenuating at the level of communities and ecosystems or, alternatively, has consistent effect sizes across increasing levels of ecological organisation. We address this question using a field‐based manipulation of assembly history of wood‐inhabiting fungi. The largest effect sizes were observed for the frequency of some individual species, and mean effect sizes were lower for community metrics of fungi immigrating from the regional species pool. There was little evidence, however, of attenuation in effect sizes at the ecosystem level (carbon, nitrogen, decomposition) in comparison to the species or community level. These results indicate that assembly history can have strong effects on ecosystem properties even under natural levels of environmental variability.