The most common application of neonicotinoid insecticides in agriculture is through the treatment of seeds before planting. Commercially formulated seed treatments are often sold as mixtures of various pesticides, fungicides and other treatments (e.g., plant growth regulators), the effects of which on non-target organisms are not well understood. To address this data gap, we assessed the effects of wheat seeds coated with the neonicotinoid thiamethoxam and four fungicides on the deep-burrowing earthworm Lumbricus terrestris. In this dataset, we examined changes in physiological effects (metabolomic profiles, acetylcholinesterase activity, and oxidative stress indicators) in multiple tissues of the earthworm at the conclusion of the 3-month exposure experiment.