Yes, there's a natural intake and outtake of carbon. The plant material goes into the soil and it's used by the micro-organisms. Their process of using it exhales the carbon.
We can put a chamber on the soil and measure CO2 coming out, but it's the net balance of that input and output that we're talking about. That net input, when it's greater than the output, is a sign that carbon is being stored in the soil.