The Limone Costa d'Amalfi and Limone di Sorrento lemons from the Sorrento Peninsula have Protected Geographical Indication (PGI) and are subject to origin fraud. The 87Sr/86Sr ratio (SrIR) signature of lemons and soils was investigated to verify its reliability to trace the PGI lemons and to highlight environmental factors responsible of the lemon SrIRs. The SrIR ranges of each PGI lemon were not discriminating as they overlapped with each other and some non-PGI lemon SrIRs fell within these ranges. The lemon SrIRs were generally not correlated with bulk and bioavailable soil SrIRs, rather, they were the result of plant Sr uptake with different SrIRs depending on interaction between water supplied to soil and soil with different chemical and physical characteristics. The study of lemon SrIRs and the causes of their origin and variability provides a reliable forecast reference for the other PGI agri-food products in the study area. •Lemon 87Sr/86Sr ratios were not exhaustive for origin discrimination.•Lemon 87Sr/86Sr ratios were not significantly correlated with those of soils.•Lemon 87Sr/86Sr ratios depended by rainwater, sea spray, irrigation water and soil.•87Sr/86Sr ratio trends in lemons and soils depended on volcanic soil properties.•87Sr/86Sr ratios of Sorrento peninsula, Vesuvius, Sele Plain soils were achieved.