Arbuscular mycorrhizal fungi (AMF) favored the accumulation of secondary metabolites in leaves of lettuces in previous studies. When fertilized with selenium (Se), mycorrhizal lettuces had more proteins, sugars and minerals than non-mycorrhizal ones. However, Se contents were lower in mycorrhizal plants suggesting a negative correlation between Se and AMF applications. The aim of the present study was to test if Se fertilization interfered with AMF technology for enhancing secondary metabolites in lettuces. Green and red-leaf lettuces were or not inoculated with AMF and received or not different selenocompounds. Flavonols and anthocyanins were non-destructively measured. At harvest, growth, water status, chlorophylls, carotenoids, phenolics and antioxidant capacity were determined. In green-leaf lettuces Se application counteracted benefits of AMF on chlorophylls and carotenoids and decreased phenolics. In red-leaf lettuces, sodium selenite positively interacted with AMF in enhancing flavonols, but imidoselenocarbamate reduced flavonols in mycorrhizal plants. No significant interaction between AMF and Se was detected for the total antioxidant capacity in leaves of both types of lettuces. The efficiency of mycorrhizal technology for improving antioxidant compounds in the edible tissues of lettuces can be modified under Se fertilization, being the interaction positive or negative depending on lettuce cultivar, antioxidant compound and chemical form of selenocompound.