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Background: Phytolith-occluded carbon (PhytOC) is highly stable and constitutes an important long-term carbon pool in agroecosystems, particularly in nutrient-poor, sandy soils. Silicon (Si) uptake by plants is strongly associated with phytolith formation, with Si accounting for up to 90% of phytolith composition. However, the role of Si fertilization in enhancing PhytOC sequestration under field conditions remains insufficiently quantified. Integrated fertilization strategies supporting sustainable development in climate-resilient agriculture can enhance biological carbon sequestration by increasing phytolith formation and phytolith-occluded carbon accumulation, thereby improving the carbon sink potential of cereal-based agroecosystems. Methods: A field experiment was conducted to assess phytolith and PhytOC accumulation in barley biomass under different fertilization regimes, including foliar silicon application using the liquid immune stimulant Optysil and compost fertilization. Phytolith content was determined separately for grain and straw, and PhytOC stocks were converted into CO2 equivalents to estimate annual sequestration potential. Results: Barley produced substantial amounts of phytoliths, with consistently higher concentrations in straw than in grain. Phytolith content ranged from 18.46 to 21.28 mg g−1 DM in grain and from 27.89 to 38.97 mg g−1 DM in straw. Depending on fertilization treatment, annual carbon sequestration through PhytOC ranged from 16.86 to 55.17 kg CO2 equivalents ha−1. Foliar silicon application increased PhytOC accumulation in barley biomass by up to threefold compared with treatments without Si. Conclusions: The results demonstrate that optimizing silicon fertilization can substantially enhance carbon sequestration in cropping systems via phytolith formation and PhytOC stabilization. Given the dominant role of cereals in crop rotations and their high phytolith-producing capacity as monocotyledonous plants, Si-mediated PhytOC sequestration represents a promising pathway for strengthening soil carbon storage and contributing to climate change mitigation.