The genetic basis of the resistance of potatoes to Phytophthora infestans is well-studied. Plant resistance to P. infestans is genetically controlled, and secondary metabolites play a role, but the metabolites themselves (e.g., phenylpropanoids) are poorly understood. This study aimed to characterize the effects of two P. infestans isolates and host resistance on secondary metabolite expression in potato plants. To do this, the phenylpropanoid pathway, chlorogenic acid, flavonoids, salicylic acid and jasmonic acid elicitors were characterized. The late blight-susceptible potato cultivar (Jutlandia) responded to both isolates with changes in the levels of compounds in the early phenylpropanoid pathway, whereas the response of the resistant cultivar (Toluca) occurred later in the pathway and was more marked in the case of the A2 mating-type isolate. The results reveal important differences in the role of secondary metabolism in resistance to P. infestans and suggest that different phenylpropanoids are affected depending on the isolate and the host's susceptibility to P. infestans.