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Carbonates interfere with soil aggregation in semi-arid calcareous soils, promoting the stability of macroaggregates and decelerating the decomposition of the organic matter within them. Our aim was to determine the process through which carbonates participate in aggregation. We hypothesised (i) a tendency to accumulate reactive clay minerals via Ca2+ bridging, and (ii) a precipitation of carbonates within aggregates due to dissolution/re-precipitation phenomena. The <250-mu m fractions of a Typic Calcixerept (CALC) and a decarbonated Calcic Haploxerept (DECALC) were incubated from the same agricultural field in semi-arid Spain with added maize straw during 28 days. A size-based fractionation was used to separate different aggregates in incubated and field-moist samples, and aggregates were analysed for organic C and maize-derived C, clay mineralogy by X-ray diffraction, and micromorphology in digital images of thin sections. Contrary to the first hypothesis, the two soils showed a similar tendency to accumulate smectite in aggregates, probably because the cation exchange capacity was saturated by Ca2+ in both CALC and DECALC. Macroaggregates showed a less porous structure in CALC than in DECALC due to the accumulation of calcite microcrystals, as formulated in the second hypothesis. We propose that low porosity of macroaggregates is mainly responsible for the slower turnover of organic matter observed in CALC than in DECALC. These results explain the greater concentration of organic C in microaggregates within macroaggregates in field-moist samples in CALC than in DECALC. The different porosity of macroaggregates may also result in differences in physical properties between CALC and DECALC. These observations suggest a different response of calcareous soils in terms of organic matter protection, resistance to erosion, and water storage compared with other soil types in semi-arid lands.