Soil structure formation in alluvial soils is a fundamental process in near-natural floodplains. A stable soil structure is essential for many ecosystem services and helps to prevent river bank erosion. Plants and earthworms are successful soil engineering organisms that improve the soil structural stability through the incorporation of mineral and organic matter into soil aggregates. However, the heterogeneous succession of different textured mineral and buried organic matter layers could impede the development of a stable soil structure. Our study aims at improving the current understanding of soil structure formation and organic matter dynamics in near natural alluvial soils. We investigate the effects of soil engineering organisms, the composition, and the superimposition of different alluvial deposits on the structuration patterns, the aggregate stability, and organic matter dynamics in in vitro soil columns, representing sediment deposition processes in alluvial soils. Two successions of three different deposits, silt–buried litter–sand, and the inverse, were set up in mesocosms and allocated to four different treatments, i.e. plants, earthworms, plants + earthworms, and a control. X-ray computed tomography was used to identify structuration patterns generated by ecosystem engineers, i.e. plant root galleries and earthworm tunnels. Organic matter dynamics in macro-aggregates were investigated by Rock-Eval pyrolysis. Plant roots only extended in the top layers, whereas earthworms preferentially selected the buried litter and the silt layers. Soil structural stability measured via water stable aggregates (%WSA) increased in the presence of plants and in aggregates recovered from the buried litter layer. Organic matter dynamics were controlled by a complex interplay between the type of engineer, the composition (silt, sand, buried litter) and the succession of the deposits in the mesocosm. Our results indicate that the progress and efficiency of soil structure formation in alluvial soils strongly depends on the textural sequences of alluvial deposits.