Vegetation cover can affect the lithological mapping capability of space- and airborne instruments because it obscures the spectral signatures of the underlying geological substrate. Despite being widely accepted as a hindrance, few studies have explicitly demonstrated the impact vegetation can have on remote lithological mapping. Accordingly, this study comprehensively elucidates the impact of vegetation on the lithological mapping capability of airborne multispectral data in the Troodos region, Cyprus. Synthetic spectral mixtures were first used to quantify the potential impact vegetation cover might have on spectral recognition and remote mapping of different rock types. The modeled effects of green grass were apparent in the spectra of low albedo lithologies for 30%–40% fractional cover, compared to just 20% for dry grass cover. Lichen was found to obscure the spectra for 30%–50% cover, depending on the spectral contrast between bare rock and lichen cover. The subsequent impact of vegetation on the remote mapping capability is elucidated by considering the outcomes of three airborne multispectral lithological classifications alongside the spectral mixing analysis and field observations. Vegetation abundance was found to be the primary control on the inability to classify large proportions of pixels in the imagery. Matched Filtering outperformed direct spectral matching algorithms owing to its ability to partially unmix pixel spectra with vegetation abundance above the modeled limits. This study highlights that despite the limited spectral sampling and resolution of the sensor and dense, ubiquitous vegetation cover, useful lithological information can be extracted using an appropriate algorithm. Furthermore, the findings of this case study provide a useful insight to the potential capabilities and challenges faced when utilizing comparable sensors (e.g., Landsat 8, Sentinel-2, WorldView-3) to map similar types of terrain.