Anaerobic digestion is increasingly used in Europe to treat organic substrates and produce biogas as a renewable energy source. The residual matter (digestate) is used in agriculture as an organic fertilizer. The study aims at assessing the impact of digestate application in the field on earthworms from the short term (few hours) to the long term (two years), and at investigating under laboratory conditions the role of ammonia and earthworm behavior on digestate toxicity in the short term. First, we studied earthworm communities in fields fertilized with digestates, cattle effluents, or chemical fertilizers for two years. Earthworm abundance was assessed before and after the fertilization event of the third year. Earthworm mortality at the soil surface was also assessed immediately after fertilization. Next, the toxicity of digestate or ammonia solutions on Aporrectodea caliginosa and Lumbricus terrestris was measured in microcosms (110 cm3) to better understand the short-term toxicity (two weeks). Finally, we spread digestate (40–80 t ha−1) on soil columns (5300 cm3) and used X-ray tomography after two weeks to assess the burrowing behavior of earthworms in the cores. Earthworm abundance was 150% higher in the fields treated for two years with digestates or cattle effluents compared to the field treated with chemical fertilizers. 0.5 to 2% of adult earthworms died at the soil surface a few hours after liquid digestate and cattle slurry spreading (18 to 24 t ha−1). The digestate (10% to 20% (fresh digestate/dry soil)) and ammonia were also lethal to earthworms in the microcosms within two weeks. In contrast, no mortality occurred inside soil columns two weeks after digestate spreading; A. caliginosa avoided the soil surface with high digestate inputs. This case study highlighted the potential short-term toxicity of digestate (a few hours), which evolved towards a neutral to positive impact in the field in the longer term (from two weeks to two years). Further research is needed to understand the impact of diverse solid and liquid digestates on soil macrofauna in different soils.