Intensive agricultural management affects the physical, chemical, and biological properties of soil, potentially contributing to a decrease in soil carbon storage. In this study, the effects of soil management intensity on soil organic carbon (SOC) content and its labile fractions, i.e., water-soluble organic carbon (OC-sol) and permanganate oxidizable carbon (POXC), were evaluated in a volcanic-ash-derived soil (Andisol) with a very high soil organic matter (SOM) content (>20%). These indicators were associated with water-stable aggregates (WSAs) and biological indicators, namely, earthworm density, cellulase activity, and autoclaved-citrate-extractable (ACE) proteins, related to the decomposition of SOM and its physical protection. The conditions evaluated were secondary native forest (SF), naturalized grassland (NG), no-till (NT), and conventional tillage (CT), considering the last item to be representative of a higher agriculture management intensity. Soil samples were collected by horizon. The SF and NG soil showed higher contents of SOC, OC-sol, and POXC. When comparing the evaluated annual cropping systems, NT showed higher values than CT (p < 0.05) in the first horizon (Hz1), while similar values were found at deeper horizons. The highest cellulase activity, ACE protein levels, and earthworm densities were found in NG and SF. NT also showed significantly higher levels of the aforementioned factors than CT (p < 0.05). A positive and significant relationship was found between the SOC content and WSA (R² = 0.76; p < 0.05) in the whole profile and between POXC and WSA for Hz1 (R² = 0.67; p < 0.05). Soil C storage was affected by the intensity of agricultural management, mainly because of the effect of tillage on structural stability, considering that biological activity synthesizes compounds such as enzymes and proteins that react and adhere to the mineral fraction affecting aggregate stability. The C content stored in the soil is consequently a key indicator with which to regulate SOM and protect SOC.