This study investigates the darkening processes affecting Maros-Pangkep rock art through a comprehensive multianalytical approach. We integrate in-situ color index measurements using Nix color Pro 2 with various physicochemical characterization techniques, including optical microscopy, XRF, SEM-EDS, Raman spectroscopy, and FTIR. By examining microbial, geochemical, and anthropogenic factors on rock art pigment samples, we establish a clear correlation between the formation of blackish-gray layers and reduced chromaticity values, indicating a significant darkening process. The shift in pigment color from vibrant red or purple to a prevailing blackish-gray hue is attributed to surface accumulation. Surface morphology analysis reveals distinct blackish deposits and delicate white fibrous structures on darkened rock art. Elemental composition analysis demonstrates heightened blackish deposit formation and increased phosphorus content in darkened samples. SEM-EDS characterization exposes gypsum morphology, with filament-like structures prevailing in heavily darkened samples, highlighting the role of both geochemical and microbial factors in deposit layer formation. FTIR spectra results confirm the presence of gypsum minerals, which are attributed to the substrate minerals and/or mineral weathering product, and unveil the existence of organic compounds, indicating microbial activity. Additionally, Raman spectroscopy reveals the anthropogenic contribution, notably soot deposition produced by human activities, to the darkening of rock art. This study underscores the need for a holistic preservation approach addressing natural, human, and microbial impacts on cultural heritage sites. Further research is also needed to conduct cross-sectional stratigraphical analysis to understand the accurate mechanism of the deterioration process on the rock art. Moreover, excavation measures regarding the possible relationship of soot deposition with human activities are also important to be carried out at the sites.