Enhancing the productivity of sandy soils requires external inputs of organic matter and nutrients, yet the molecular-level transformations of soil organic matter (SOM) following amendments remain unclear. This study investigated these changes using soil samples from a 77-day pot trial with hydrotalcite, bentonite, zeolite, compost, and biochar amendments. SOM was extracted using accelerated solvent extraction and analyzed by gas chromatography-mass spectrometry (GC-MS) to compare molecular compositions between amended and control soils. Results showed that amendments enriched pre-existing SOM with a diverse range of organic compounds, including fatty acids, n-alkanes, alcohols, sugars, esters, amino acids, and aromatics. Biochar-amended soils exhibited the highest concentrations of alcohols, fatty acids, sugars, and esters, that may suggest improved bacterial and fungal growth. These compounds may then leach into surrounding soil further improving conditions for microbial growth. Mineral-amended soils also showed a notable increase in organic compounds. While no direct addition of organic matter occurred in these treatments, the observed changes in SOM composition suggest that these amendments may enhance microbial processing of existing organic carbon. The findings indicate that amendments contribute to greater molecular diversity in SOM, with potential implications for soil health and stability. However, the long-term stability of these changes needs to be assessed to determine whether the increased organic compounds have solely positive effects or if any potential negative impacts may arise over time. Understanding these transformations is critical for evaluating the long-term effects of amendments on soil functionality. By revealing the molecular dynamics of carbonaceous organic matter in amended soils, this study contributes to the development of more effective soil management strategies to improve fertility and resilience in sandy soils.