Mineral alteration is a possible side effect of spectroscopic techniques involving laser ablation, such as laser-induced breakdown spectroscopy (LIBS), and is related to the interaction of the generated plasma and ablated material with samples, dust, or ambient atmosphere. Therefore, it is essential to understand these interactions for analytical techniques involving laser ablation, especially for space research. In this combined LIBS–Raman analytical study, pyrite (FeS2) and pyrrhotite (Fe1–xS) samples have been consecutively measured with LIBS and Raman spectroscopy, under three different atmospheric conditions: ∼10–4 mbar (atmosphereless body), ∼7 mbar, and Martian atmospheric composition (Martian surface conditions), and 1 bar and Martian atmospheric composition. Furthermore, a dust layer was simulated using ZnO powder in a separate test and applied to pyrite under Martian atmospheric conditions. In all cases, Raman spectra were obscured after the use of LIBS in the area of and around the formed crater. Additional Raman transitions were detected, associated with sulfur (pyrite, 7.0 mbar and 1.0 bar), polysulfides (all conditions), and magnetite (both minerals, 1.0 bar). Magnetite and polysulfides formed a thin film of up to 350–420 and 70–400 nm in the outer part of the LIBS crater, respectively. The ZnO-dust test led to the removal of the dust layer, with a similar alteration to the nondust pyrite test at 7.0 mbar. The tests indicate that recombination with the CO2-rich atmosphere is significant at least for pressures from 1.0 bar and that plasma–dust interaction is insignificant. The formation of sulfur and polysulfides indicates fractionation and possible loss of volatile elements caused by the heat of the LIBS laser. This should be taken into account when interpreting combined LIBS–Raman analyses of minerals containing volatile elements on planetary surfaces.