The phenomenon of musical consonance is an essential feature in diverse musical styles. The traditional belief, supported by centuries of Western music theory and psychological studies, is that consonance derives from simple (harmonic) frequency ratios between tones and is insensitive to timbre. Here we show through five large-scale behavioral studies, comprising 235,440 human judgments from US and South Korean populations, that harmonic consonance preferences can be reshaped by timbral manipulations, even as far as to induce preferences for inharmonic intervals. We show how such effects may suggest perceptual origins for diverse scale systems ranging from the gamelan’s slendro scale to the tuning of Western mean-tone and equal-tempered scales. Through computational modeling we show that these timbral manipulations dissociate competing psychoacoustic mechanisms underlying consonance, and we derive an updated computational model combining liking of harmonicity, disliking of fast beats (roughness), and liking of slow beats. Altogether, this work showcases how large-scale behavioral experiments can inform classical questions in auditory perception.