Phytolith-occluded carbon (PhytOC) is highly stable, and constitutes an important source of long-term C storage in agrosystems. This stored carbon is resistant to the processes of oxidation of carbon compounds. In our research phytolith content in barley (Estonia) and oat (Poland) grain and straw was assessed at field trials, with Si as a liquid immune stimulant OPTYSIL and compost fertilisation. We showed that cereals can produce relatively high amounts of phytoliths. PhytOC plays a key role in carbon sequestration, particularly for poor, sandy Polish and Estonian soils. The phytolith content was always higher in straw than in grain regardless of the type of cereals. The phytolith content in oat grains varied from 18.46 to 21.28 mg∙g−1 DM, and in straw 27.89–38.97 mg∙g−1 DM. The phytolith content in barley grain ranged from 17.24 to 19.86 mg∙g−1 DM, and in straw from 22.06 to 49.08 mg∙g−1 DM. Our results suggest that oat ecosystems can absorb from 14.94 to 41.73 kg e-CO2∙ha−1 and barley absorb from 0.32 to 1.60 kg e-CO2∙ha−1. The accumulation rate of PhytOC can be increased 3-fold in Polish conditions through foliar application of silicon, and 5-fold in Estonian conditions. In parallel, the compost fertilisation increased the phytolith content in cereals.