Plant-associated microorganisms can help crops to alleviate stress and increase the resilience of agricultural ecosystems to climate change. However, we still lack knowledge on the dynamics of soil and plant microbiomes and their response to changing conditions. This information is essential for the development of microbiome-based solutions to improve crop resilience to stressors associated with climate change. In this work, we explored: (i) the conformation of the bacterial and fungal assemblages of different soil and plant compartments (bulk soil, rhizosphere, roots, leaves and grains) along the crop cycle of maize in an open field trial; and (ii) the effect of water restriction on the maize microbiome, comparing optimal irrigation with a 30% reduction of water supply. Our results show a dynamic compartment-driven recruitment of microorganisms with contrasting patterns for bacteria and fungi that were intensified towards the end of the plant cycle. Roots showed the most differentiated bacterial assemblage while fungi conformed a very distinct community in the leaves, suggesting a relevant contribution of aerial fungal propagules to the microbiome of this plant organ. Regarding the grain, bacterial communities looked closer to those in the leaves, while fungal communities were more like those in the root. Despite the reductions in plant growth and yield, the microbiome of limited-watered plants did not show severe alterations. Still, significant impacts were observed within compartments, being fungi more responsive to limited watering than bacteria, with hallmark fungal ASVs for each compartment and irrigation regime. Network analysis suggests that bacteria and fungi may play different roles in the shifts observed under water limitation. Our study highlights the importance of conducting multikingdom analyses for a holistic understanding of the dynamics and evolution of the microbial assemblages in the whole plant and their roles in plant response to environmental stressors.