In potato (Solanum tuberosum) crops, the use of fungicides to control some diseases is widespread; however, it has been reported that this practice can modify the potato polyphenolic content, and new strategies oriented to the potato defense system are necessary. One alternative is the use of arbuscular mycorrhizal fungi (AMF) to improve the defense mechanisms of plants. In this study, phenolic profiles and antioxidant activities in leaves of three potato genotypes (CB2011-509, CB2011-104, and VR808) were evaluated in crops inoculated with three AMF strains (Claroideoglomus claroideum, Claroideoglomus lamellosum, and Fumneliformis mosseae) and with AMF in combination with the use of two commercial fungicides (MONCUT [M] and ReflectXtra [R]). Eight phenolic compounds were detected, mainly hydroxycinnamic acids (HCAD) and flavonols, in samples where the highest concentrations of HCAD were obtained, 5-caffeoylquinic acid was the most abundant phenolic. The antioxidant activity was higher using the cupric reducing antioxidant capacity (CUPRAC) and ferric reducing antioxidant power (FRAP) methods. The association of AMF with plants had benefits on the secondary metabolism; however, the response differed according to genotype. The different combinations of potato genotypes, AMF strain, and fungicide modified the content of phenolic compounds in leaves in different ways; the treatment using C. lamellosum and ReflectXtra was the ideal combination for the genotypes analyzed here, with the higher antioxidant response, which supports the further technological evaluation of efficient AMF strains and fungicides in potato crops.