The pea aphid (Acyrthosiphon pisum) is a complex of at least 15 genetically different host races that are native to specific legume plants but can all develop on the universal host plant Vicia faba. Despite much research, it is still unclear why pea aphid host races can accept and colonize their native host plants while non-native host races are not. To determine the changes in the host plant chemistry and their possible influence in the specificity of the pea aphid host races, we used several metabolomics aproaches on full factorial experimental set ups by infesting separately four different plant species (Medicago sativa, Trifolium pratense, Pisum sativum, and Vicia faba) with native and non-native pea aphid clones of various host races. Our results from the non-targeted and targeted approaches suggested that the plant species investigated have developed different complexities of chemicals to defend themselves from the attack of herbivores including phloem feeders. Our results also suggested that A. pisum clones have evolved different feeding strategies to manipulate the host plant defense signaling, reduced deterrence or toxicity, improved host quality, reduction of enemies, and improved quality of future food sources in the vicinity to perform better on these plants. We have selected a group of polar and non-polar secondary metabolites that might be associated with the discrimination and compatibility of the pea aphid host races with the different legume species used in this project. However, additional experimentation is necessary to fully understand the effects and influence of these compounds in the specificity of the pea aphid host races.