Berries of Vitis vinifera L. cv. Merlot, grown on a neutral or calcareous soil, were infected, at phenological phases of veraison and ripening, by a conidial suspension of Aspergillus carbonarius to control ochratoxin A production and trans-resveratrol- and epsilon-viniferin-induced synthesis as affected by the soil lime content. Chlorosis occurrence was evaluated by a visual rating scale at veraison, and the leaves from vines growing on the calcareous soil showed the typical yellowing, whereas those grown on the neutral soil were dark green. Berry mineral element yield was recorded at veraison and ripening. Infection symptoms on berries were more severe at ripening in bunches collected from vines grown in calcareous soil. Ochratoxin A concentration increased at phenological phase of veraison in berries harvested from vines cultivated in calcareous soil. A. carbonarius enhanced trans-resveratrol and epsilon-viniferin production in infected berries more than in the control samples. Moreover, at veraison their concentration in the berries collected from vines grown in calcareous soil was greater than that recorded from berries collected from vines grown in the neutral soil. The lowest symptom severity was observed on berries containing the highest copper concentration.