A growing body of research analyzing musical scores suggests mode’s relationship with other expressive cues has changed over time. However, to the best of our knowledge, the perceptual implications of these changes have not been formally assessed. Here, we explore how compositional choices of 17th- and 19th-century composers (J. S. Bach and F. Chopin, respectively) differentially affect emotional communication. This novel exploration builds on our team’s previous techniques using commonality analysis to decompose intercorrelated cues in unaltered excerpts of influential compositions. In doing so, we offer an important naturalistic complement to traditional experimental work—often involving tightly controlled stimuli constructed to avoid the intercorrelations inherent to naturalistic music. Our data indicate intriguing changes in cues’ effects between Bach and Chopin, consistent with score-based research suggesting mode’s “meaning” changed across historical eras. For example, mode’s unique effect accounts for the most variance in valence ratings of Chopin’s preludes, whereas its shared use with attack rate plays a more prominent role in Bach’s. We discuss the implications of these findings as part of our field’s ongoing effort to understand the complexity of musical communication—addressing issues only visible when moving beyond stimuli created for scientific, rather than artistic, goals.