This paper focuses on the spectral characteristics of lobate ejecta across Syrtis Major volcano, a dark region of Mars presenting a mafic composition as revealed from the Observatoire pour la Minéralogie, l'Eau, les Glaces et l'Activité (OMEGA) instrument. Two spectrally distinct crater types are identified. Type I is enriched in high-calcium pyroxene (HCP) relative to the volcanic rocks. Type II is similar to the lava flow mineralogy driven by HCP, compared to the Noachian crust dominated by low-calcium pyroxene (LCP). Type I craters are systematically younger than type II. The type II mineralogy has been likely affected by a long-term weathering in a cold environment for the last 2 Ga. The axisymmetric spectral signatures of type I ejecta appear dominated by rock-forming minerals rather than by soils and reflect the composition of excavated materials offering a window for exploring the subsurface. A progressive change in the slope of the spectra around 1.5–2 μm is observed across the ejecta layers, pointing at a change in the HCP/LCP ratio. The deconvolution of the spectra by the Modified Gaussian Model unravels a maximum of HCP/LCP band strength ratio located between 1.2 and 3 crater radii for all type I craters. Using Z-modeling, this observation translates into a maximum in the HCP/LCP abundances at a few hundreds of meters depth and suggests a homogeneous subsurface structure of the volcanic edifice. Below this horizon the HCP/LCP decrease may reveal a more ancient lava composition or the signature of the underlying Noachian crust.