The distribution of ‘Candidatus Phytoplasma prunorum’, a phloem-limited pathogen, varies among plant tissues during the year, but knowledge about quantitative comparisons of its presence in roots and above-ground tissues across Prunus species remains limited. The variation in ‘Ca. P. prunorum’ in four Prunus species was monitored monthly during 2025 using quantitative PCR-based absolute quantification. Roots, one-year-old shoots and annual shoots were sampled monthly from 21 infected trees of Prunus armeniaca, Prunus domestica, Prunus persica and Prunus salicina. Phytoplasma titer varied with plant part and sampling month, and differences were also observed among the examined host groups. Because cultivar and rootstock were linked to species, these differences cannot be attributed to species alone. Roots provided the most consistent year-round detection, whereas above-ground tissues showed stronger monthly variation during the studied period. P. domestica displayed the most distinct pattern: roots remained frequently positive, while one-year-old shoots and particularly annual shoots had lower detection rates and lower phytoplasma titers. Multilocus genotyping detected ten multilocus profiles, but their uneven distribution among only 21 trees precluded a reliable evaluation of their relationship with phytoplasma titer or symptom expression.