Soft X-ray photoelectron spectroscopy (SXPS) and energy-scanned photoelectron diffraction (PhD) have been used to study the surface species produced by exposure of Ru(0001) to methanol at ~ 150 K. SXPS shows a single surface species is formed at sub-monolayer coverages with an O 1s peak binding energy of ~ 532.6 eV, 2.8 eV greater than that of chemisorbed atomic oxygen. O 1s PhD data from this species shows no significant modulations, in contrast to simulated PhD spectra from a methoxy species occupying a three-fold coordinated hollow site, as predicted by earlier density functional theory calculations, or atop or bridging sites. By contrast, PhD data from the O 1s of the atomic oxygen species in the Ru(0001)(2 × 1)–O phase are consistent with the oxygen atoms occupying ‘hcp’ hollow sites (above second-layer Ru atoms) at a Rusingle bondsingle bondO bondlength of 2.01 ± 0.02 Å, essentially identical to previous structure determinations of this phase. O 1s PhD recorded at normal emission from adsorbed CO are also consistent with the known CO atop adsorption species. We conclude that the methanol-derived surface molecular species is not methoxy in a well-defined local site on the surface, but is consistent with clusters of intact methanol identified in a recent infrared spectroscopy investigation.