Solanum tuberosum is one of the most important crops in the world; however, drought has caused significant losses in its production. One solution is the use of arbuscular mycorrhizal fungi (AMF). In this study, the phenolic profiles and antioxidant activity of the leaves of two potato genotypes (VR808 and CB2011-104) were evaluated over time in crops inoculated with two strains of AMF, as well as a consortium, in combination with a commercial fungicide. In addition, three usable humidity levels were established after the beginning of tuberization. The phenolic compounds found during the first sampling time in the VR808 genotype reached a maximum of 3348 mg kg−1, and in the CB2011-104 genotype, they reached a maximum of 2982 mg kg−1. Seven phenolic compounds were detected in the VR808 genotype, and eleven were detected in the CB2011-104 genotype, reaching the highest concentration at the last sampling time. The antioxidant activity in the first sampling was greater than the Trolox equivalent antioxidant capacity (TEAC), and in the third sampling, the cupric reducing antioxidant capacity (CUPRAC) predominated. The association of AMF with the plant by PCA demonstrated that these fungi assist in protecting the plants against water stress, since in the last harvest, the results were favorable with both mycorrhizae.