Ecologists have documented the process of plant succession for centuries, yet the successional patterns exhibited by the associated microbial communities have received relatively little attention. Plants form microhabitats for a large diversity of microbiota that offer significant benefits to their host plants. To date, microbial succession in plants was mostly studied on the rhizosphere and phyllosphere compartment where community structure is initially determined by stochastic processes. In addition to the horizontal transmission of microbiota from the surrounding environment, plant-associated microbiota is also transferred vertically directly from parent to offspring via the seeds. By its nature, this inherited microbiota might be selected and transmitted over generations and provide valuable and lasting benefits to its host plant. However, little is known about the contribution of seed-borne endophytes over time when microbiota from the external environment will also colonize the seedling host, leading to shifts in microbial community structure during seedling ontogeny. In ENDOSHIFT, we will explore patterns of microbial succession over plant ontogeny, and how environmental conditions change microbial assemblages and dynamics. To do this, we will set up a greenhouse experiment to detail the successional progression of the microbiota across the root and leaf endosphere, and the rhizosphere compartments during plant ontogeny. Seeds of a single mother plant will be sown among two soil treatments and two water supply and the different plant compartments will be sampled at 10 time points over 120 days. Leaf and root traits will be measured to characterise the plant phenotype and assessment of the microbiota (i.e., bacteria and fungi) in the different plant compartments will be analysed and quantified using high-throughput sequencing and droplet digital PCR, respectively. Our results will contribute novel insights into the dynamics of microbial assemblage over plant ontogeny and environmental changes while providing a fundamental knowledge base on bacterial and fungal taxa associated with roots and leaves. ENDOSHIFT will ultimately lead to a better grasp of the influence of plant-associated microbiota on the host fitness and on our ability to predict plant establishment and regeneration in natural heterogeneous ecosystems.