Intercropping is a powerful way to promote a more diversified plant community in the field, thereby enabling complementary and facilitative relationships. In these systems, legumes are a key functional group, and are highly valued for the agroecological services they provide. This review identifies the different complementarity and facilitation processes in soils in intercropped legume/cereal systems and the key role of soil microorganisms in these processes. The intercropped legumes/cereal systems reduce inter-specific competition by enhancing complementarity/facilitation processes thereby improving the exploitation of resources, which is, in turn, reflected in the increase in plant production corresponding to greater efficiency of the agroecosystem as a whole. Plant production, including above-and belowground biomass, is positively correlated with microbial abundance and diversity. This microbial life is assumed to play a significant role in the availability and transfer of soil nutrients to plants as well as in plant health and soil fertility. Although we are currently unable to identify a reliable and exhaustive pattern of plant-microbe interactions, perhaps simply because no universal relationship exists between plants and microorganisms, reliable scenarios reveal strong trends and define the conditions required for successful intercropping systems and microbial interactions. Given our incomplete knowledge of facilitation processes and belowground interactions, intercropping systems must learn from and apply the experience gained in successful experiments. Intercropping dynamics play a critical role in explaining the establishment of facilitative root interactions and finally suggest perennial plant associations may be more effective than annual ones.