To further our understanding of the role of perceptual processes in musical emotions, we investigated individuals with congenital amusia, a neurodevelopmental disorder that alters pitch processing. Amusic and matched control participants were studied for emotion recognition and emotion intensity ratings of both musical excerpts and faces. Emotion recognition was found to be impaired in amusic participants relative to controls for the musical stimuli only. This impairment suggests that perceptual deficits in music processing reduce amusics’ access to a verbal and conscious representation of musical emotions. Nevertheless, amusics’ performance for emotion recognition was above chance level, and multidimensional scaling (MDS) analyses revealed that their categorization of musical pieces was based on similar representation spaces of emotions as for control participants. The emotion intensity ratings, nonverbal and possibly more implicit than the categorization task, seemed to be intact in amusic participants. These findings reveal that pitch deficits can hinder the recognition of emotions conveyed by musical pieces, while also highlighting the (at least partial) dissociation between emotion recognition and emotion intensity evaluation. Our study thus sheds light on the complex interactions between perceptual and emotional networks in the brain, by showing that impaired central auditory processing partially alters musical emotion processing.