Introduction Fine lavender and lavandin are perfume and medicinal plants originate from the South of France and are widely cultivated for their essential oils. Recently, cultivated plants suffered from a severe decline in France, due to the propagation of the yellow decline disease. This disease is caused by the stolbur phytoplasma, a bacterium transmitted by a sap-sucking insect, the planthopper. Objectives In order to understand the complex relationships between host plant, pest, pathogen and environment responsible for the yellow decline of lavender, we use a metabolomic approach to highlight changes in chemical emissions from asymptomatic ("healthy") and symptomatic ("infected") plants. Methods Volatile compounds produced by fine lavender and lavandin were collected in the field using a dynamic head-space extraction approach. Afterwards, compounds trapped on Tenax adsorbent were thermodesorbed and analysed using an automated thermal desorption-gas chromatography-mass spectrometry (ATD-GC-MS). Multivariate statistical analyses was performed using principal component analysis and partial least square discriminant analyses. Results The untargeted screening of volatiles allowed the separation of asymptomatic and symptomatic plants according to their emissions. The approach was sufficiently accurate so as to separate the emissions according to the different stages of infection. Twelve compounds were found to be deregulated metabolites of yellow disease infection, common to fine lavender (variety 7713) and lavandin (variety abrial). Conclusion The metabolomic approach allowed for the effective identification of chemical variations between infected and healthy plants in a complex field environment.