The minerals exploration undercover relies on the understanding of the ore-forming processes and the associated alteration characteristics that are used in vectoring towards a deposit. Previously, the proposed process for forming the 1590 Ma Abra base-metal deposit, hosted at 250 m depth in the Paleoproterozoic Edmund Basin of the Western Australian Capricorn Orogen, was through exhalation to the seafloor (SEDEX-style). Lacking any visible signs of alteration, sediments overlying the Abra deposit were perceived as younger, unaltered, and cutting the mineralisation and associated alteration comprised of siderite, chlorite and minor sericite. However, a recent study delineated a phengitic (i.e. Al-poor, Mg-, Fe-, Si-rich) white mica footprint in regolith above the deposit from hyperspectral field and remote sensing data. This study links the surficial mineral footprint to the deposit below through detailed analysis of hyperspectral data from drill core. The hyperspectral data processing results were validated using optical microscopy, micro-XRF and SEM-EDS analysis, and compared with geochemical, lithological and structural drill core data. Hyperspectral short-wave infrared (SWIR) data revealed a vertically zoned alteration footprint from the deposit to the surface, where very fine-crystalline phengitic white mica (i.e. sericite) and chlorite are most abundant a few tens of metres above the deposit. The abundance of chlorite gradually decreases, and the distal phengitic alteration is cut by the present erosional surface, but only moderately affected by weathering, confirming the surficial footprint detected in the previous study. Similarly, a vertically zoned carbonate alteration was delineated from thermal infrared (TIR) reflectance spectra from drill cores up to 2 km away from the deposit. Carbonate alteration from proximal to distal comprised of Mn-rich siderite, ankerite and ferroan dolomite, which replace the dolomite matrix in coarse-grained stratigraphic sequences. The replacement of dolomite matrix suggests that these permeable horizons acted as fluid conduits, which channelled hydrothermal fluids into sedimentary strata from a feeder structure. The presence of a vertically zoned carbonate and chlorite-phengite footprint in the overlying sediments advocates for their deposition before the ore formation at Abra, and a sub-seafloor replacement within a permeable sedimentary sequence as the ore-forming process. Comparable alteration footprints have been described around some world-class sediment-hosted base-metal deposits, including the Sullivan in the British Columbia, which is considered as a classic SEDEX-style by some and an exhalative-replacement hybrid by others. Also, identical footprints are common around the volcanic-hosted massive sulphide and are associated with the carbonate replacement-style deposits - an overlap which is an interesting future research space where hyperspectral technologies could provide answers. Validated hyperspectral data combined with geochemical, lithological and structural information enabled the identification of a subtle mineral footprint above the Abra deposit, and the established method can be used for vectoring towards other buried mineralisations - even through weathering.