Background: Many studies have demonstrated the benefits of long-term music training (i.e., musicianship) on the neural processing of sound, including simple tones and speech. However, the effects of musicianship on the encoding of simultaneously presented pitches, in the form of complex musical chords, is less well established. Presumably, musicians’ stronger familiarity and active experience with tonal music might enhance harmonic pitch representations, perhaps in an attention-dependent manner. Additionally, attention might influence chordal encoding differently across the auditory system. To this end, we explored the effects of long-term music training and attention on the processing of musical chords at the brainstem and cortical levels. Method: Young adult participants were separated into musician and nonmusician groups based on the extent of formal music training. While recording EEG, listeners heard isolated musical triads that differed only in the chordal third: major, minor, and detuned (4% sharper third from major). Participants were asked to correctly identify chords via key press during active stimulus blocks and watched a silent movie during passive blocks. We logged behavioral identification accuracy and reaction times and calculated information transfer based on the behavioral chord confusion patterns. EEG data were analyzed separately to distinguish between cortical (event-related potential, ERP) and subcortical (frequency-following response, FFR) evoked responses. Results: We found musicians were (expectedly) more accurate, though not faster, than nonmusicians in chordal identification. For subcortical FFRs, responses showed stimulus chord effects but no group differences. However, for cortical ERPs, whereas musicians displayed P2 (~150 ms) responses that were invariant to attention, nonmusicians displayed reduced P2 during passive listening. Listeners’ degree of behavioral information transfer (i.e., success in distinguishing chords) was also better in musicians and correlated with their neural differentiation of chords in the ERPs (but not high-frequency FFRs). Conclusions: Our preliminary results suggest long-term music training strengthens even the passive cortical processing of musical sounds, supporting more automated brain processing of musical chords with less reliance on attention. Our results also suggest that the degree to which listeners can behaviorally distinguish chordal triads is directly related to their neural specificity to musical sounds primarily at cortical rather than subcortical levels. FFR attention effects were likely not observed due to the use of high-frequency stimuli (>220 Hz), which restrict FFRs to brainstem sources.