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Heavy metal contamination in soil is increasing rapidly due to increasing anthropogenic activities. Despite the importance of rose-scented geranium as a medicinal plant, little attention was paid to enhancing its productivity in heavy metal-polluted soil. In this regard, endophytes improve plant resistance to heavy metal toxicity and enhance its tissue quality. Here, the impact of the three endophytic fungi <i>Talaromyces versatilis</i> (E6651), <i>Emericella nidulan</i>s (E6658), and <i>Aspergillus niger</i> (E6657) on geranium growth, tolerance, and tissue quality under cadmium (Cd) stress was investigated. In contrast to <i>E</i>. <i>nidulans</i>, <i>T</i>. <i>versatilis</i> and <i>A</i>. <i>niger</i> enhanced geranium growth and the stimulatory effect was more pronounced under Cd-stress. The three endophytes significantly alleviated Cd accumulation and increased mineral content in geranium leaves. In addition, endophytic fungi successfully alleviated Cd-induced membrane damage and reinforced the antioxidant defenses in geranium leaves. Inoculation with endophytes stimulated all the antioxidant enzymes under Cd-stress, and the response was more obvious in the case of <i>T</i>. <i>versatilis</i> and <i>A</i>. <i>niger</i>. To reduce the toxicity of tissue-Cd levels, <i>T</i>. <i>versatilis</i> and <i>A</i>. <i>niger</i> upregulated the detoxification mechanisms; glutathione-S-transferase, phytochelatin, and metallothionein levels. Moreover, endophytic fungi improved the medicinal value and quality of geranium by increasing total antioxidant capacity (TAC), phenolic compound biosynthesis (phenylalanine ammonia-lyase), and vitamin content as well as the quantity and quality of essential oil, particularly under Cd-stress conditions. The variation in the mechanisms modulated by the different endophytic fungi was supported by Principal Component Analysis (PCA). Overall, this study provided fundamental insights into endophytes’ impact as a feasible strategy to mitigate the phytotoxicity hazards of Cd-stress in geranium and enhance its quality, based on the growth and biochemical investigations.