The global importance of forest ecosystems for essential ecosystem services, including local livelihoods and climate change mitigation, requires a detailed understanding of the major factors determining biodiversity, health, and sustainability of forests. It has long been known that forest trees are closely associated with microorganisms, but a comprehensive description of the tree associated microbiome (hereafter referred to as plant microbiome) extending beyond the relatively well-studied root mutualists, and the understanding of its functional role is largely missing. In our viewpoint, we argue that a more comprehensive consideration of the plant microbiome, especially that of the so far neglected phyllosphere and endosphere will substantially increase the understanding of fundamental ecological processes in forest ecosystems. An explicit tree community-level approach is particularly missing in the current research efforts. Because plants and their microbiome are inseparable entities forming the plant holobiont, they may collectively determine plant community assembly, diversity, functional traits, and resulting ecosystem processes to a much stronger degree than is currently acknowledged. Here, we aim to highlight the so far underestimated importance of the plant microbiome for the structure and functioning of forest ecosystems. More specifically, we emphasize the functional diversity of the plant microbiome for a better understanding of tree community dynamics and the resulting consequences for ecosystem functioning, which appears particularly important with ongoing global change. By providing a general context of the current limitation of knowledge and indicating some specific research areas that need more attention in the future, we hope that our contribution may help in identifying current research needs and stimulate future research.