This study aimed to elucidate the insect resistance of some strains of quinoa seedlings through metabolomics and transcriptomics studies. Some quinoa strains are susceptible to the feeding of certain insects, such as Spodoptera exigua, leaving the plant leaves full of holes. However, there are some quinoa strains that have insect resistance, and thus, we studied the metabolites and gene expression profiles of insect-resistant strains for future application in plant agriculture. We believe that our study makes a significant contribution to the literature because we were able to show, through metabolomics and transcriptomics studies, the different metabolites and pathways that are expressed in insect-resistant quinoa seedling strains. This information will be useful for quinoa growers, especially so that they will know which strains to focus on in the future.