Accurate clay mineral identification is key to understanding past aqueous activity on Mars, but martian phyllosilicates are old (>3.5 Ga) and have been heavily bombarded by meteoroid impacts. Meteoroid impacts can alter clay mineral structures and spectral signatures, making accurate remote sensing identifications challenging. This paper uses nuclear magnetic resonance (NMR) spectroscopy to examine the short-range structural deformation induced in clay mineral samples of known composition by artificial impacts and calcination. Structural changes are then related to changes in the visible-near infrared (VNIR) and mid-infrared (MIR) spectra of these clay mineral samples. The susceptibility of phyllosilicates to structural deformation after experimental impacts varies by structure. Experimental results showed that trioctahedral, Mg(II)-rich saponite was structurally resilient up to peak pressures of 39.8 GPa and its unchanged post-impact spectra reflected this. Experimental data on kaolinite showed that this Al(III)-rich, dioctahedral phyllosilicate was susceptible to structural alteration at peak pressures ⩾ 25.1 GPa. This result is similar to previously reported experimental results on the Fe(III)-rich dioctahedral smectite nontronite, suggesting that dioctahedral phyllosilicates may be more susceptible to shock-induced structural deformation than trioctahedral phyllosilicates. The octahedral vacancies present in dioctahedral phyllosilicates may drive this increased susceptibility to deformation relative to trioctahedral phyllosilicates with fully occupied octahedral sheets. Thermal alteration accompanies shock in meteoroid impacts, but shock differs from thermal alteration. NMR spectroscopy showed that structural deformation in thermally altered phyllosilicates differs from that found in shocked phyllosilicates. Similar to shock, dioctahedral phyllosilicates are also more susceptible to thermal alteration. This differential susceptibility to impact-alteration may help explain generic smectite identifications from heavily bombarded terrains on Mars.