Arbuscular mycorrhizal (AM) fungi colonize the roots of most plants to establish a mutualistic symbiosis leading to important benefits for plant health. We have recently shown that AM symbiosis alters both transcriptional and hormonal profiles in tomato roots, many of these changes related to plant defence. Here, we analytically demonstrate that the levels of other important defence-related compounds as phenolic acids are also altered in the symbiosis. Both caffeic and chlorogenic acid levels significantly decreased in tomato roots upon mycorrhization, while ferulic acid increased. Moreover, in the case of caffeic acid a differential reduction was observed depending on the colonizing AM fungus. The results confirm that AM associations imply the regulation of plant defence responses, and that the host changes may vary depending on the AM fungus involved. The potential implications of altered phenolic acid levels on plant control over mycorrhizal colonization and in the plant resistance to pathogens is discussed.