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Cropland soils are key systems in global carbon budgets due to their high carbon-sequestration potential. It is widely accepted that clays are one of the soil components that have a significant effect on the stabilisation of soil organic carbon (SOC), owing to its surface interactions with organic molecules. However, the identification of the direct effects of clays on SOC stabilization is complicated, mainly due to the difficulty of accurately characterizing the mineralogy of clays, especially phyllosilicates. In this study, the relationships between soil phyllosilicates and functional SOC pools in woodlands and comparable olive groves, under two contrasting management systems (bare soils versus soil under cover crops) and parent materials (calcareous and siliceous), were explored. The total mineralogy of soil and clay fractions and the soil-clay assemblages were analysed through the decomposition of X-ray diffraction patterns, and were then related to four SOC pools. Total and unprotected SOC was higher in olive groves under cover crops, and this was true independent of the parent material, proving the importance of herbaceous covers in SOC sequestration in woody crops. Some significant correlations between clay minerals and SOC fractions were found. Interestingly, mixed-layer content was correlated with the biochemically protected SOC fraction (r = 0.810, p < 0.05), and this was so even when the partial correlation coefficient was calculated (r = 0.761, p < 0.05). According to the partial correlation networks (PCN), four separated clusters of variables were obtained, which joined into only one at fdr < 0.25. The PCNs supported the direct correlation between mixed-layer content, especially those rich in smectite, and the biochemically protected SOC fraction, suggesting that smectite layers may stabilize organic molecules. Since potassium enrichment is higher in the rooted layers of woodland and soils under cover crops, and this increase is related to the collapse of swelling layers, these soils were poorer in smectite phases than the bare soils. This also would explain why the biochemically protected SOC was more abundant in the latter. [ABSTRACT FROM AUTHOR]