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The variability in stocks and accumulation rates of organic carbon (Corg), nitrogen (N), and carbonate (CaCO3) was studied in fifteen Posidonia oceanica meadows spread throughout the South Aegean Sea (Greece). In addition, the abiotic and biotic drivers determining the pattern of variability in the accumulation rates were assessed by exploring the influence of sediment characteristics, seagrass traits, and environmental settings. The meadows supported on average (±STDEV) 14.6 ± 5.0 kg Corg m−2, 0.47 ± 0.17 kg N m−2, and 249 ± 210 kg CaCO3 m−2 in the top meter of their sediments, with mean accumulation rates over the last 500 years of 33.6 ± 23.6 g Corg m−2 yr−1, 1.00 ± 0.62 g N m−2 yr−1, and 405 ± 336 g CaCO3 m−2 yr−1 across sites. A redundancy analysis (RDA) explained 70% of the variation in Corg, N, and CaCO3 accumulation rates, with three sediment characteristics (i.e., sediment Corg:N and Corg:Cinorg ratios and P. oceanica contribution to the sediment Corg pool) emerging as the primary set of factors shaping the accumulation of matter, followed by seagrass traits (i.e., leaf biomass and rhizome elongation) and environmental variables (i.e., suspended organic matter). The high degree of variability within the region emphasizes the need for fine‐scale assessments to understand the local conditions influencing sequestration. Our findings underscored the critical role of seagrass meadows in carbon and nitrogen sequestration in the region, urging conservation efforts to protect these ecosystems and prevent potential losses of stored carbon and nitrogen following seagrass degradation. Plain Language Summary: In the present study, we explored the abiotic and biotic factors influencing the accumulation patterns of carbon, nitrogen, and carbonate in 15 seagrass (Posidonia oceanica) meadows across the South Aegean Sea (Greece). Sediment characteristics (i.e., sediment Corg:N and Corg:Cinorg ratios and P. ocenica contribution to the sediment Corg pool) mainly drove the pattern of carbon, nitrogen, and carbonate accumulation, with seagrass traits (i.e., leaf biomass and rhizome elongation) and environmental conditions (i.e., suspended organic matter) contributing to a lesser extent. Overall, seagrass meadows play a crucial role in storing carbon and nitrogen in the studied region, serving as important natural sinks, and thus, protecting these ecosystems is important to prevent the loss of these stored elements. Additionally, understanding the factors that shape the variability in Posidonia oceanica storage capacity is crucial for management and conservation efforts. Key Points: Seagrass (Posidonia oceanica) meadows of the South Aegean Sea (Greece) represent important natural sinks for organic carbon, nitrogen, and carbonate.The accumulation pattern of organic carbon, nitrogen, and carbonate in the underlying seagrass sediments was mainly driven by sediment characteristics, followed by seagrass traits and environmental conditions.Fine‐scale assessments are crucial for understanding the local factors shaping the storage capacity of seagrass meadows to support management decisions. [ABSTRACT FROM AUTHOR]