To help solve the actual problem of global climate warming, it is important to comprehensively study soil organic carbon (SOC), soil fungi, and other parameters at different depths in the soil. This study was aimed at investigating the chemical and microbiological parameters and their interactions at various soil depths (0–5 to 195–200 cm) in an Arenosol in a Scots pine stand in southwestern Lithuania, with a focus on the main groups of fungi and their influence on SOC. The highest diversity of soil fungi species was found at a depth of 50–55 cm. Saprotrophs were dominant at all investigated soil depths. Ectomycorrhizal fungi were mostly abundant at depths of up to 50–55 cm. The C:N ratio gradually decreased down to 50–55 cm, then increased in deeper soil layers (from 50–55 to 195–200 cm). This means that the most active mineralization processes occur at depths of between 0 and 55 cm. Carbon stabilization processes occur at depths of 100–105 to 195–200 cm, and most of this carbon does not enter the atmosphere nor contribute to the process of climate change.