Crops absorb carbon dioxide from the air. That's a very important point, because it's photosynthesis that limits the carbon that's available to build the carbon in the soil. It's only when the carbon is sequestered in the soil that it's considered taken out long enough, because everything that crops produce eventually gets consumed by a cow, or by people and is transferred back to CO2.
In a sense, it doesn't count, but the part that gets sequestered in the soil is the part that counts.