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The host-pathogen combinations—Malus domestica (apple)/`Candidatus Phytoplasma mali´, Prunus persica (peach)/`Ca. P. prunorum´ and Pyrus communis (pear)/`Ca. P. pyri´ show different courses of diseases although the phytoplasma strains belong to the same 16SrX group. While infected apple trees can survive for decades, peach and pear trees die within weeks to few years. To this date, neither morphological nor physiological differences caused by phytoplasmas have been studied in these host plants. In this study, phytoplasma-induced morphological changes of the vascular system as well as physiological changes of the phloem sap and leaf phytohormones were analysed and compared with non-infected plants. Unlike peach and pear, infected apple trees showed substantial reductions in leaf and vascular area, affecting phloem mass flow. In contrast, in infected pear mass flow and physicochemical characteristics of phloem sap increased. Additionally, an increased callose deposition was detected in pear and peach leaves but not in apple trees in response to phytoplasma infection. The phytohormone levels in pear were not affected by an infection, while in apple and peach trees concentrations of defence- and stress-related phytohormones were increased. Compared with peach and pear trees, data from apple suggest that the long-lasting morphological adaptations in the vascular system, which likely cause reduced sap flow, triggers the ability of apple trees to survive phytoplasma infection. Some phytohormone-mediated defences might support the tolerance., Author summary Tons of fruits get lost each year by pathogenic phytoplasma infections of stone and pome fruit trees worldwide. Besides clearing infected trees, no effective control strategies are available and more specific studies are mandatory to enhance pest managements. Whereas phytoplasma genome sequencing has stimulated the deciphering of molecular mechanisms, the process of physiological and morphological responses of host plants is poorly understood. This is the first comprehensive and precise study on the influence of specific phytoplasma species on the vascular system and leaf phytohormone levels of their Rosaceae host plants (apple, peach and pear) at the same time. This study reveals anatomical and physiological changes in apple trees, which may result from an enhanced ability to sense phytoplasma infection and provoke adequate and successful cellular and physiological defence responses. In contrast, peach and pear trees seem to miss this ability, causing the often-observed fast death of infected trees. The study provides new and important insights into the phytoplasma-induced diseases and symptom development. Improved understanding of the diseases is vital for the development of sustainable pest management strategies and breeding resistant cultivars.