Background and aims <p>The succession process of new coastal bare land in river deltas into mature terrestrial ecosystems remains unclear. Quantitatively describing succession trajectories over long timescales helps understand biodiversity maintenance, restoration, and soil carbon storage in estuarine deltas.</p> Methods <p>In the Yellow River Delta (prograding since 1855), we traced historical river course shifts (P1: 1976–2020; P2: 1953–1964; P3: 1929–1934; P4: 1904–1929) and sampled four alluvial sectors. By controlling for the sea-land distance gradient of 0, 10, 20, and 30&#xa0;km, we constructed a continuous time series to analyze the dynamics of ecological properties.</p> Results <p>The new coastal bare land soils exhibit high organic matter storage at a depth of 1&#xa0;m but underwent degradation during stage P1, accompanied by reduced microbial species richness. Inland regions exhibited lower salinity and faster vegetation development compared to nearshore zones, with these differences becoming more pronounced over a century. From stage P2 to P4, 0–20&#xa0;cm soil organic matter accumulated significantly over time (<i>R</i>² &gt; 0.5) except for the 0&#xa0;km gradient, following the recovery of microbial species richness. Microbial community dissimilarity linearly accumulated with succession age (<i>R</i>² &gt; 0.4). Structural equation models indicated that the recovery of soil organic matter and microbial species richness over time is driven by vegetation development.</p> Conclusions <p>Vegetation drives the recovery of soil organic matter and microbial species richness after river flow diversion but is inhibited by salinity. Succession age accounts for 4.65% and 4.28% of the unique variation in bacterial and fungal communities, respectively.</p> Graphical Abstract <p></p>