Increased crop production is a main goal to feed the predicted human population in future. The current management practice is, however, not sustainable as it depends on high amounts of fertilizer application and is highly vulnerable to decreased soil water availability. At the same time it becomes more and more crucial to reduce or even mitigate anthropogenic greenhouse gas (GHG) emissions. A possible way to enable this, might be the increase of the soil C sequestration and thus the C sink function of arable lands. A recent and potentially more sustainable idea is the single time fertilization with amorphous silicon (ASi) which is known to increase both nutrient and water availability. Here we show for the first time on the basis of a field plot experiment how a fertilization with ASi is affecting both, crop yield and the C sequestration of the soils in an agricultural system cultivating wheat. We found a strong increase in wheat yield and biomass production after ASi fertilization by increasing soil moisture during the whole growing season. Additionally, despite a relatively short growing season, Si fertilization increased the net C uptake by soils, i.e., C sequestration with both Si fertilized treatments showing a negative net ecosystem C balance (soil C gain) during the measurement period, while the control showed a small positive net ecosystem C balance (soil C loss). To our best knowledge, this is the first time such effect has ever been observed. In summary, our study demonstrates a new management strategy for crop production increasing yield and biomass production as well as soil C uptake on a more sustainable basis, by a single time fertilization with ASi.