Evaluating the fertility of agricultural soils through biodiversity is essential for sustainable agriculture. Using biochar, compost and their combination become an option to increase soil fertility and rehabilitate degraded land. However, the potential negative effect of these amendments remains poorly understood. This study explored the risks associated with biochar and compost using the earthworm Eisenia Andrei, a key soil organism and bioindicator, exposed to biochar 2% (20gkg^-1 soil), and compost 1% (10gkg^-1 soil) and their mixture in two soil types (organic and conventional) for 7 and 14 days. To assess cytotoxic and genotoxic effects, lysosomal membrane stability (LMS) and micronucleus (MNi) assays were performed. Biochemical biomarkers, including catalase (CAT), glutathione S-transferase (GST), malondialdehyde (MDA), and acetylcholinesterase (AChE) for neurotoxicity, were analyzed. additionally, earthworm gut metabolomic profiles were examined. Our Results revealed a significant decrease in lysosomal membrane stability (LMS) and an increase in DNA damage (MNi). Neurotoxicity responses varied between organic and conventional soils. Biochemical analysis indicated oxidative stress, as presented by alterations in CAT, GST, and MDA, with the strongest effects observed under combined biochar–compost exposure in both soil types. Moreover, biochar and compost significantly modulated metabolites associated with oxidative stress, inflammatory processes, amino acid biosynthesis, energy metabolism, and nucleic acid pathways, with stronger perturbations under co-exposure. Overall, these findings provide new insights into the toxic mechanism of biochar and compost exposure in earthworms, and highlight the role of the soil management practices in biological responses from multiple perspectives.