Climate change will threaten the ecosystems on which humans depend for healthcare. This phenomenon will be especially pronounced for populations of developing countries who depend on medicinal and aromatic plants (MAPs) as first medications. During the last decade, several MAPs were included to the French Pharmacopeia and obtained marketing authorizations based on assertions for anti-inflammatory properties. Biotic and abiotic factors were shown to influence both MAPs growth and specific metabolites content. Increases in atmospheric CO2 and temperature or drought are major climatic disturbances that have variable consequences depending classes of metabolites. On the other hand, arbuscular mycorrhizal fungi (AMF) may induce changes in specific metabolites of MAPs by activating metabolic pathways. Clinical study showed evidence of anti-inflammatory effects of MAPs, however they often considered single herbal compound omitting the complex combination contributing to the holistic effects of MAPs. AMF are obligate symbionts having a huge potential to improve plant growth by different mechanisms, including increased mineral nutrition, water uptake, drought and disease resistance and plant productivity in exchange for carbon. Two metabolomic approaches based on Proton nuclear magnetic resonance and high-resolution mass spectrometry could lead to the discovery of new patterns in the biotic and abiotic interactions. A research consortium including four institutes and a private partner with complementary expertise was set up to understand the impact of climate change on MAPs metabolome and anti-inflammatory activities of MAPs and evaluate AMF as regulator of environmental stress.