The plant microbiome consists of the combined microbial communities that reside on and within the plant; these communities have an intrinsic relationship with their hosts, and some confer benefits to the plant host. This work aimed to investigate different soybean microbial communities' spatial and temporal colonisation patterns and their overall ecological assembly processes. The overarching hypothesis was that there are spatial and temporal microbial niches spaces within the soybean microbiome, and these niche spaces are under strict plant-mediated selection. It highlighted those interactions between spatial and temporal dynamics influenced microbiome diversity patterns. Moreover, it emphasised the existence of a strong temporal dependence of communities. Using complementary community assembly models, I highlighted that the plant compartment and developmental stage modulated the balance between niche-based and neutral processes. Also, it showed the importance of dispersal limitations in structuring plant microbiomes. Lastly, I highlighted that the seed microbiome colonised the shoot compartment during early developmental stages, whilst the soil microbiome colonised the rhizosphere. The seed microbiome was capable of outcompeting members of the rhizosphere to colonise the endophytic space quickly. Different microbiome sources also influenced the abundance of N-cycling genes across all plant compartments, with an increased abundance of N-cycling genes in the soil treatment. Overall, this thesis shows that the soybean microbiome is temporally nested, and microbiome sources influenced colonisation patterns. Lastly, plant-mediated selection along with dispersal limitation played a role in their assembly. This knowledge adds to ongoing efforts to manipulate plant microbiomes for increased beneficial services and more sustainable agriculture.