<p>Rare earth elements (REEs), comprising the lanthanides, scandium, and yttrium, are increasingly released into the environment due to anthropogenic activities but are not routinely monitored as conventional environmental contaminants. Gadolinium (Gd), used as a contrast agent in magnetic resonance imaging, is continuously discharged into aquatic ecosystems. While Gd effects on plants have been partially explored, its impact on plant physiology and plant-microbiome interactions remains poorly understood. This study investigated the effects of 150 µM Gd (23.6 mg L^− 1, 23.6 ppm) on tomato plants (<i>Solanum lycopersicum</i> L.) grown in hydroponics using a phosphate-free nutrient solution to prevent Gd precipitation and ensure its bioavailability. A multidisciplinary approach was employed, integrating morphological, physiological, biochemical, and molecular analysis. Plant growth, root system architecture, antioxidant defence responses, calcium content, Gd accumulation and translocation were assessed, together with changes in the composition and predicted functional potential of the rhizosphere microbiome. Prolonged Gd exposure significantly impaired tomato growth reducing leaf fresh weight from 7.90&#xa0;g in control plants to 3.15&#xa0;g in treated seedlings and markedly altering root morphology. Stress conditions triggered strong oxidative responses, while Gd accumulated predominantly in roots (5.32 mg g^− 1), with no detectable translocation to aerial tissues. Rhizosphere microbial community composition was severely altered (e.g., Burkholderiales declined to 42% in Gd-treated plants). This work represents one of the first integrated assessments of plant morphological, physiological, biochemical and microbiome-level responses of a crop plant and its rhizosphere microbiome to Gd exposure, providing new insights into the ecological and agronomic implications of emerging REEs contamination.</p>