Distractor-response binding (DRB) has been widely studied to understand the interplay between perception and motor processes, with DRB effects referring to performance costs or benefits that arise when previously co-occurring distractors and responses are retrieved together. We hypothesize that musical training and musical perception skills modulate flexibility in reconfiguring auditory perception–action associations; this has not yet been investigated in the context of DRB. Here, we use an auditory DRB paradigm with concomitant EEG recordings to investigate how auditory-motor bindings are established, retrieved, and how they might differ between harmonic versus inharmonic sounds. Using a healthy sample of participants (N = 42) with a wide range of musical training, we also investigated whether these processes are modulated by musical perception skills, assessed using the well-established Micro-PROMS (Profile of Music Perception Skills). Behavioral and EEG results indicated significant DRB effects for both harmonic and inharmonic distractor sound combinations. These effects were modulated by harmonicity: stronger behavioral DRB effects and weaker DRB effects in theta band activity were found when inharmonic as compared to harmonic distractor stimuli were presented. Beamformer analysis localized the theta band effect to the right superior temporal cortex, highlighting the role of this brain area in auditory-motor integration. Further, this study provides evidence that participants with better musical perception skills and higher cumulative practice time show increased flexibility in handling perception–action associations. Together, these findings enhance the understanding of how auditory stimuli interact with motor actions, particularly in relation to individual differences in musical perception skills.