This ability triggers once for each -1/-1 counter. For example, if Leech Bonder (a creature that enters with two -1/-1 counters on it) entered, Flourishing Defenses's ability would trigger twice.

This ability triggers both when a -1/-1 counter is put on a creature on the battlefield and when a creature enters with a -1/-1 counter on it. This includes when a creature returns to the battlefield as a result of persist.