Microorganisms may enhance plant resilience to water stress by influencing their hosts’ physiology and anatomy at the leaf-level. Bacterial and yeast endophytes, isolated from wild poplar and willow, can improve the intrinsic water-use efficiency (iWUE) of cultivated poplar (Populus) under water-deficits by lowering stomatal conductance (gsw). However, the relevance of stomatal anatomy underlying this reduction remains unclear. We hypothesized endophyte inoculation could change host stomatal anatomy, and this would relate to decreases in gsw. We subjected Salicaceae endophyte-inoculated and uninoculated Populus trichocarpa to well-watered and water-deficit treatments in greenhouse studies. We examined the changes of individual stomatal traits and related the composition of these parameters, termed stomatal patterning, to leaf gas-exchange under light saturation. After a water-deficit, inoculation improved iWUE at light saturation from preserving carbon assimilation (Anet) and lowering gsw, but these changes were independent of soil-moisture status. Drops in gsw corresponded to underlying shifts in stomatal patterning. Inoculated plants had smaller, more compact stomata and greater anatomical maximum stomatal conductance (gsmax) relative to the control. Salicaceae endophytes may alter stomatal density and size, lowering gsw and increasing iWUE. Future efforts may quantify endophyte colonization of the host to draw direct relationships between microbes and stomatal traits.