The Ħal Saflieni Hypogeum is a unique subterranean Maltese Neolithic sanctuary with a well-documented history of interest in its acoustics (Till, 2017; Debertolis et al., 2015; Reznikoff, 2014; Devereux, 2009; Skeates, 2008; Mifsud and Mifsud 1999; Devereux, 1996; Evans, 1971; Zammit, 1910; Griffiths, 1920). Previous studies have noted its unusual strongly-defined frequency spectrum (Debertolis et al., 2015), but it is unknown if this was coincidental. In this paper, we present evidence that the Hypogeum's creators shaped the site's geometry to create or amplify its frequency spectrum, or another property closely correlated with the spectrum. Specifically, we show that the observed spectrum required jointly fine-tuning the dimensions of multiple non-contiguous cave walls across multiple independent chambers, to a degree that seems unlikely to be coincidental. We also note that the peak frequencies are evenly spaced and resemble a whole-tone scale in music, which is also unlikely to be coincidental and suggests the spectrum itself might have held some cultural significance. Taken together, it suggests acoustic or spectral properties may have played a motivational or cultural role for the site's Neolithic creators. This work identifies one of the earliest known examples of a manmade structure with a significant musical element to its interior architecture.