This paper presents an architecture for the creation of emotionally congruent music using machine learning aided sound synthesis. Our system can generate a small corpus of music using Hidden Markov Models; we can label the pieces with emotional tags using data elicited from questionnaires. This produces a corpus of labelled music underpinned by perceptual evaluations. We then analyse participant’s galvanic skin response (GSR) while listening to our generated music pieces and the emotions they describe in a questionnaire conducted after listening. These analyses reveal that there is a direct correlation between the calmness/scariness of a musical piece, the users’ GSR reading and the emotions they describe feeling. From these, we will be able to estimate an emotional state using biofeedback as a control signal for a machine-learning algorithm, which generates new musical structures according to a perceptually informed musical feature similarity model. Our case study suggests various applications including in gaming, automated soundtrack generation, and mindfulness.