The amygdala is important for reward-associated learning, but how distinct cell groups within this heterogeneous structure are recruited during appetitive learning is unclear. Here we used Fos induction to map the functional amygdalar circuitry recruited during early and late training sessions of Pavlovian appetitive conditioning. We found that a number of distinct amygdalar nuclei were differentially recruited by tone-food pairings during the early and late stages of training, suggesting evidence of learning-induced plasticity. Notably, these selectively activated nuclei belong to dissociable subsystems that are well placed to simultaneously inform cortical (cognitive) processing and behavioral control during tone-food learning.