During learning of a sensory discrimination task, cortical and sub-cortical regions display complex spatiotemporal dynamics. During learning, both amygdala and cortex link stimulus information to its appropriate association, for example a reward. In addition, both structures are also related to non-sensory parameters such as body movements and licking during the reward period. However, the emergence of cortico-amygdala relationships during learning is largely unknown. To study this, we combined wide-field cortical imaging with fiber photometry to simultaneously record cortico-amygdala population dynamics as male mice learn a whisker-dependent go/no-go task. We were able to simultaneously record neuronal populations from the posterior cortex and either the basolateral amygdala (BLA) or central medial amygdala (CEM). Prior to learning, somatosensory and associative cortex responded during sensation, while amygdala areas did not show significant responses. As mice became experts, amygdala responses emerged early during the sensation period, increasing in CEM, while decreasing in BLA. Interestingly, amygdala and cortical responses were associated with task-related body movement, displaying significant responses ∼200 ms before movement initiation which led to licking for the reward. A correlation analysis between cortex and amygdala revealed negative and positive correlation with BLA and CEM respectively, only in the expert case. These results imply that learning induces an involvement of cortex and amygdala which may aid to link sensory stimuli with appropriate associations.Significance Statement Levitan and Gilad study neuronal dynamics in cortex and amygdala as mice learn a sensory discrimination task. They find that amygdala areas display opposing responses only after the mice learn the task. In contrast cortical areas display responses both before and after learning. These results imply that learning induces an involvement of amygdala and cortical areas in order to optimally link sensory stimuli with appropriate associations.