Aggregation in soils is the result of the interaction of the soil organic components and soil minerals. The reactivity of the mineral phase is acknowledged to interfere with aggregates formation and stabilization, but its influence on aggregation in semi-arid Mediterranean soils remains mostly unknown. In this study, we used micromorphological analysis of aggregates formed in a 28-d incubation in two agricultural soils differing only in the composition of the mineral phase in the upper Ap horizon (a carbonate-depleted Palexeralf with 21.5% clay, and a contiguous carbonate-rich Typic Calcixerept with 20.9% clay before decarbonation which was reduced to 10.4% upon decarbonation). The two soils belong to the same agricultural field and have had similar management for decades. Soil samples were completely disaggregated into their fractions < 250 μm, and incubated with fresh organic matter to stimulate re-aggregation. Macroaggregates (> 2 mm) formed during the incubation were separated at days 3, 7, 14, 21 and 28 and used to prepare thin sections. Macroaggregates were more abundant at day 3, and then decreased in number in the two soils, which indicates a dependency between organic matter decomposition and stable macroaggregates formation. They contained a greater proportion of smaller aggregates in the decarbonated soil. Micromorphological analysis revealed significant differences in the fabric and physical characteristics of these macroaggregates, in which bonds among primary particles were observed to be led by clays in the Palexeralf while the coarse fraction appeared embedded in a micromass with crystallitic b-fabric corresponding to carbonates in the Calcixerept. This resulted in a more compact fabric and less porosity in macroaggregates in the Calcixerept. Image analysis of thin sections was used to quantify and characterize the pore system of macroaggregates. Porosity (pores > 20 μm) was more than double (36.9% for 15.6%) within macroaggregates in the decarbonated soil, with more elongated pores. Although in both soils most pores were 20 to 150-μm in equivalent diameter, some porosity > 150 μm was observed only in macroaggregates from the decarbonated soil. These observations allow hypothesizing that the mechanisms responsible for aggregates stabilization and/or formation are different in the two soils, and that they result in different physical characteristics of soil aggregates. The implications of such differences on air and water flow rates within aggregates, and thus on the soil microbial activity and organic matter decomposition, as well as on soil erodibility, need to be studied and accounted for when evaluating the effect of soil management and other practices on soil quality in semi-arid Mediterranean agrosystems.