Understanding metabolite changes and underlying metabolic pathways that may be affected in target plants following essential oils (EOs) exposure is of great importance. In this study, a gas chromatography-mass spectrometry (GC/MS) based metabolomics approach was used to determine the metabolite changes in lettuce (Lactuca sativa L.) shoot and root after exposure to different concentrations of W. trilobata EO. Multivariate analyses of principal component analysis (PCA) and orthogonal partial least-discriminant analysis (OPLS-DA) corroborated that shoot and root of lettuce responded differently to W. trilobata EO. In EO-exposed shoot samples, an increase in the levels of malic acid, glutamine, serine, lactose and α-glucopyranose affected important metabolism pathways such as glycolysis, fructose and mannose metabolism and galactose metabolism. The findings suggest that lettuce may be up-regulating these metabolites to increase tolerance against W. trilobata EO. In EO-exposed root samples, changes in fatty acid biosynthesis, elongation, degradation, phenylalanine, tyrosine and tryptophan metabolism were linked to a decrease in lyxose, palmitic acid, octadecanoic acid, aspartic acid, phenylalanine and myo-inositol. These results indicate that W. trilobata EO could cause alterations in fatty acid compositions and lead to inhibition of roots growth. Together, these findings provide insight into the metabolic responses of lettuce upon W. trilobata EO exposure, as well as potential mechanisms of action of W. trilobata EO as bio-herbicides.