In potato crops, fungicides are applied to inhibit diseases produced by pathogens of fungal origin. The use of fungicides in crops can affect arbuscular mycorrhizal fungi (AMF), which have been reported to confer various benefits on plant metabolism. In this sense, it is necessary to evaluate at the physiologic and metabolic levels the effects of plant-AMF symbiosis in Solanum tuberosum crops treated with fungicides to improve growth, nutrition, and stress tolerance in potato crops. This study evaluates the effect of three strains of AMF on the radical exudation of low molecular weight organic acids (LMWOA) in the rhizosphere and antioxidant defense system, photosynthetic pigments, and photosynthetic rate on potato leaves treated with fungicides Moncut and ReflectXtra in three potato genotypes (VR808, CB2011-509, and CB2011-104). Oxalic acid was detected as the only LMWOA exuded. In general, no clear effects on the photosynthetic state of the different potato cultivars were observed. The increases were mainly provided by Funneliformis mosseae and ReflectXtra, and the VR808 genotype was found to be more metabolically affected; however, the contributions to the increases were given by specific associations between genotype-AMF-fungicide. These results were not entirely significant and had no correlation, suggesting that AMF can interfere with other mechanisms that are not enzymatic defenses under stress by fungicides; these enzymatic responses are a mechanism that is not relevant in potatoes. This study provides new information on the potato defense system and photosynthesis efficiency to improve the quality of these crops under stress conditions.