Significant losses of grains and seeds stored without any type of protection against pests and diseases cause economic losses that undermine the subsistence of small farmers, especially in regions with a low technological level. Agricultural practices free of pesticides and herbicides require new technologies to protect seeds, and in this context the use of essential oils has been widely studied. The essential oil of lemongrass has low market value and can be a viable alternative, as hypothesized in this article. To test this hypothesis, we evaluated the biochemical aspects of exposing the target insect (cowpea weevil) to the essential oil. Furthermore, we evaluated the protection afforded by coating cowpea seeds with the essential oil in function of storage time. The results confirmed the alteration of the metabolic profile, with reduction of some important amino acids and organic acids (proline, glycine, alanine) and lower expression of enzymes such as hexokinase (HK), lactate dehydrogenase (LDH) and malate dehydrogenase (MDH). These results indicated that the toxic effect of the lemongrass essential oil was a consequence of the action on the insect’s metabolism. Furthermore, the results showed that the coating with the essential oil assured a content of citral on the seed surface sufficient to provide protection from 30 and 90 days after seed treatment, and does not impact its germination power. Lemongrass essential oil showed toxic activity against phytopathogenic fungi, and no toxic activity against yeasts. Therefore, we confirm the potential of lemongrass essential oil to protect cowpea grain and seeds against insects and opportunistic phytopathogens. More details of the results are presented in the article.