Listening to music prompts strong emotional reactions in the listeners but relatively little research has focused on individual differences. This study addresses the role of musical preference and familiarity on emotions induced through music. A sample of 50 healthy participants (25 women) listened to 42 excerpts from the FMMS during 8 s while their autonomic and facial EMG responses were continuously recorded. Then, affective dimensions (hedonic valence, tension arousal, and energy arousal) and musical preference were rated using a 9-point scale, as well as familiarity using a 3-point scale. It was hypothesized that preferred and familiar music would be evaluated as more pleasant, energetic and less tense, and would prompt an increase of autonomic and zygomatic responses, and a decrease of corrugator activity. Results partially confirmed our hypothesis showing a strong effect of musical preference but not familiarity on emotion correlates. Specifically, musical preference predicted valence ratings, as well as HR acceleration and facial EMG activity. Overall, current findings suggested a great influence of musical preference on music-induced emotions, particularly modulating hedonic valence correlates. Our findings add evidence about the role of individual differences in the emotional processing through music and suggest the importance of considering those variables in future studies.