Earthworms play an important role in soil organic matter (SOM) dynamics and soil structure formation, including soil porosity and aggregate stability. Earthworms feed on organic inputs such as crop residues (CR) which are displaced by mouldboard ploughing. In a 61-day mesocosm experiment, we investigated the effects of CR placement (surface-applied vs. incorporated) and different earthworm species (combinations) on: 1) the survival and biomass of the earthworm species Lumbricus terrestris, L. rubellus, and Aporrectodea caliginosa, representing anecic, epigeic and endogeic ecological groups, respectively; and 2) earthworm-mediated soil structure formation. Earthworms were present either as single species or as species mixtures combining anecics with each of the other groups. Incorporating CR reduced biomass of surface-feeders (L. terrestris: −30% of initial body weight vs. −9% when CR were surface-applied; L. rubellus: −74% vs. −24%, respectively). L. rubellus survival was also lower when CR were incorporated (50%) than when CR were surface-applied (92%). In surface-applied CR treatments, the amount of particulate organic matter (POM) > 250 μm in the soil profile was positively affected by L. terrestris in the soil upper 20 cm by 16.5%. A similar but weaker effect was found when CR were incorporated (9% increase). Large water-stable macroaggregates (>2000 μm) increased in the upper 20 cm soil only when CR were surface-applied and L. terrestris was present (from 2.7 to 13.1 g kg−1). Small water-stable aggregates increased with functional groups interactions at all soil depths, irrespective of the CR placement. Surface-applied CR increased soil porosity at 2.5–10 cm depth. Large water-stable macroaggregate formation by earthworms was hampered through the incorporation of CR, although CR incorporation increased porosity between 2.5 and 30 cm soil depth despite reduced earthworm biomass. Furthermore, small macroaggregate formation was hampered by single species, whereas combining functional groups stimulated their formation. Under field conditions residue incorporation might result in trade-offs between the contribution of surface-feeding earthworms to soil porosity and i) their fitness, as surface-feeding earthworms' body weight loss was larger than when crop residues were surface-applied; as well as ii) large water-stable macroaggregates formation, as no increase in those was found when CR was incorporated.