Water deficit stress is considered one of the most important factors limiting maize production. Exposure to longer-term water deficit stress conditions inhibits growth and leads to yield loss. Less understood is the response of maize roots and their associated microbial communities to water deficit stress and water recovery. Toward this goal, a growth chamber experiment was conducted to characterize the response of maize seedlings under water deficit and recovery conditions. We specifically focused on maize seedling response following the V3-V4 growth stages as upon reaching these stages, maize seedlings shift their nutritional dependence from kernel reserves to the nodal root system for development, and water stress during this vegetative phase can significantly reduce overall grain yield. Furthermore, as root-associated microbes, particularly fungi, play vital roles in enhancing the water and nutrient uptake and overall seedling performance of their hosts, a secondary objective was to explore any relationships between root-associated fungal communities (i.e., inoculated vs. non-inoculated) and maize growth under both water deficit and water recovery conditions. Overall, water deficit stress reduced stomatal conductance, shoot and root growth, specific leaf area, leaf N concentration, and specific root length in maize seedlings. However, under water recovery conditions, growth of seedlings in the presence of root-associated fungi were similar to well-watered conditions over time. Changes in the composition of root-associated fungal communities under water recovery conditions resulted in increased above- and below-ground tissues and leaf N concentration of seedlings. Taken together, our results provide insight into the water deficit stress response of maize and suggest that under water recovery conditions, beneficial outcomes on maize seedlings are mediated through the effects of belowground fungal mutualists.