Due to difficulties in tracing engineered nanoparticles (ENPs) in complex media, there are few data on the exposure of soil biota to ENPs. This study used neutron activated cobalt (Co NPs) and silver (Ag NPs) nanoparticles, as well as soluble cobalt and silver salts, to assess the uptake, excretion and biodistribution in the earthworm Eisenia fetida. Concentrations of cobalt in worms after four weeks exposure reached 88% and 69% of the Co ions and Co NPs concentrations in food, respectively, while corresponding values for Ag ions and Ag NPs were 2.3% and 0.4%. Both Ag ions and Ag NPs in earthworms were excreted rapidly, while only 32% of the cobalt accumulated from Co ions and Co NPs were excreted within four months. High accumulation of cobalt was found in blood and in the digestive tract. Metal characterization in the exposure medium was assessed by sequential extraction and ultrafiltration. The Co NPs showed significant dissolution and release of ions, while Ag ions and particularly Ag NPs were more inert.