Microcomputed tomography (mu CT) is a nondestructive X-ray imaging method used in plant physiology to visualize in situ plant tissues that enables assessments of embolized xylem vessels. Whereas evidence for X-ray-induced cellular damage has been reported, the impact on plant physiological processes such as carbon (C) uptake, transport, and use is unknown. Yet, these damages could be particularly relevant for studies that track embolism and C fluxes over time. We examined the physiological consequences of mu CT scanning for xylem embolism over 3 mo by monitoring net photosynthesis (Anet), diameter growth, chlorophyll (Chl) concentration, and foliar nonstructural carbohydrate (NSC) content in 4 deciduous tree species: hedge maple (Acer campestre), ash (Fraxinus excelsior), European hornbeam (Carpinus betulus), and sessile oak (Quercus petraea). C transport from the canopy to the roots was also assessed through 13C labeling. Our results show that monthly X-ray application did not impact foliar Anet, Chl, NSC content, and C transport. Although X-ray effects did not vary between species, the most pronounced impact was observed in sessile oak, marked by stopped growth and stem deformations around the irradiated area. The absence of adverse impacts on plant physiology for all the tested treatments indicates that laboratory-based mu CT systems can be used with different beam energy levels and doses without threatening the integrity of plant physiology within the range of tested parameters. However, the impacts of repetitive mu CT on the stem radial growth at the irradiated zone leading to deformations in sessile oak might have lasting implications for studies tracking plant embolism in the longer-term.|Monthly application of X-rays reduces radial growth and deforms stems in some deciduous tree species but has little impact on other physiological functions over a growing season.