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Understanding the complex interplay of biotic and abiotic controls on soil organic carbon (SOC) stabilization and aggregate formation is a vital and evolving research field, with implications for C and climate change modeling. Here, we delve into the effects of temperature and moisture treatments on aggregate SOC composition. Aggregate fractions representing different levels of physical protection for SOC were isolated three times during a 6-month incubation with 2x2 factorial temperature and moisture treatments (22 or 30 °C, 45% or 65% water-filled pore space). The chemical composition within each fraction was analyzed using high-resolution Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) to evaluate the prevalence of different classes of C compounds by fraction and temperature and moisture treatments. In addition, a partial least square regression (PLSR) was used to explore potential correlations between relative abundance of C compound classes and C content within aggregate fractions. We found that organic matter in the macro- (>250 µm) and micro-aggregates (53 to 250 µm) was relatively enriched in lipid-, carbohydrates-, and protein--like compounds compared to silt and clay fractions (<53 µm). Organic matter in silt and clay was, on the other hand, relatively enriched in compounds with no specific classification, with overall high aromaticity. Broadly, simpler, low-molecular-weight C storage was altered by both temperature and moisture, while complex C storage was especially altered by moisture, within aggregates. Univariate effects of temperature and moisture on specific compound classes varied by soil fraction, but across fractions temperature increased the relative abundance of condensed- and unsaturated hydrocarbon-, tannin-, and amino sugar-like compounds and decreased the relative abundance of protein-like compounds. Moisture increased tannin-, condensed hydrocarbon-like compounds, and the overall aromaticity, and had the most pronounced effect in fractions occluded within macroaggregates, suggesting that substrate diffusion and pore connectivity within the aggregate environment drive the composition of C protected within aggregates. The PLSR indicated that treatments promoted different compounds to contribute to C accrual. Under dry conditions, condensed hydrocarbon-like compounds were associated with microaggregates, while amino sugar-like compounds were associated with macroaggregates and coarse particulate organic matter (POM), and lipid-like and aliphatic compounds were associated with silt and clay. Temperature effects on PLSR results were most visible in silt and clay fractions, where carbohydrate- and tannin-like compounds were associated with C content. This suggests that warmer conditions under climate change may more substantially alter mineral-associated C content, while changing water regimes will alter C content in physically protected environments, with the most significant changes under cool and moist conditions. Overall, our data reveal distinct resource pools in different climate and aggregate environments, a baseline for our understanding of SOC accrual and soil structure under different conditions. More research into how microbes process physically protected SOC under altered environments may fine-tune our ability to predict soil functions including water behavior and nutrient release.