Essential oils (EOs) are actively investigated as an alternative to numerous synthetic biocide products. Due to their large spectra of biological activities, the impact of EOs on non-target organisms should be characterized for biopesticide development purposes. In this study the potential phytotoxicity of Cinnamomum cassia EO (CEO) on apple trees (Malus domestica) was investigated in terms of oxidative burst (glutathione redox state) and damage (malondialdehyde). At 2%, CEO concentration the reduced glutathione leaf content drops from 269.6 ± 45.8 to 143 ± 28.4 nmol g−1FW, after 30 min, illustrating a rapid and strong oxidative burst. Regarding oxidative damage, malondialdehyde increased significantly 24 h post application to 10.7 ± 3.05 nmol g−1FW. Plant defence induction was previously suspected after trans-cinnamaldehyde (CEO main compound) application. Therefore, the elicitor potential was investigated by qRT-PCR, on the expression level of 29 genes related to major defence pathways (PR protein, secondary metabolism, oxidative stress, parietal modification). Multivariate analysis and increased expression levels suggest induction of systemic resistance. Hence, the present research illustrates the dose–dependent phytotoxicity of CEO in terms of lipid peroxidation. Transcriptional data illustrates the elicitor properties of CEO. These findings can help to design pest management strategies considering both their risks (phytotoxicity) and benefits (defence activation combined with direct biocide properties).