While having distinct niches, plants and earthworms have occupied soils over geological times, mutually influencing each-others. These macroorganisms are considered “ecosystem engineers”, actively modifying soil physical structure, which notably provides specific habitats for microorganisms: the rhizosphere and the drilosphere (casts/burrows produced by earthworms). In this study, we aimed to disentangle the relative importance of both macroorganisms in shaping microbial community assembly in different soil types, and determine the extent and modalities of how rhizosphere and drilosphere communities may coalesce with each-other when both plants and earthworms are present. We investigated the presence/absence influence of barley and an endogeic earthworm (Aporrectodea caliginosa) on microbial communities in three fertility-contrasted soils (sandy, loamy, clayed) using sixty microcosms over one month. Ninety-six samples were collected in distinct habitats (bulk soil, rhizospheres, casts). 16S-rRNA gene amplicon sequencing revealed that community assembly in habitats was driven by the mutual presence of both macroorganisms, with stronger effects in nutrient-poor soils. While plants’ influence was always observed, earthworms’ effect was soil-dependent. Distinct microbial groups were identified in each habitats, responding to the additional presence of the other macroorganisms. Notably, 481 OTUs from five families were always increased in both habitats when macroorganisms were combined. A soil-wide correlation network of phylogenetically related OTUs was commonly found in both rhizospheres and drilospheres, suggesting microbial interactions at the interface between these macroorganisms. Results support the hypothesis of a collaborative shaping of microbial communities by plants and earthworms, resulting in the existence of a core microbiota of their interaction in soils.