The spatial arrangement and pore size distribution play an important role in accumulation and protection of exogenous organic matter (EOM) in the soil, but how different organic materials contribute to modify pore structure is poorly understood. We aimed at exploring possible changes in the complexity of the soil phase during fertilization with different doses of digestate and sludges sourced from the agro-food industry. For this purpose, the short-term effects—one year, of soil fertilization, were investigated in several sampling periods and within two depths (0–25 cm and 25–40 cm). Changes in the specific surface area (SSA), total pore volume (VMIP), total pore area (SMIP), average pore radius (RMIP) and pore size distribution (PSD) were monitored using N2 adsorption/desorption (NAD) and mercury porosimetry (MIP) methods. Our results showed that the intensity of observed changes depended on the type and dose of organic material, soil depth and sampling date. Accumulation of EOM increased with soil depth, masking a large proportion of SSA. Deeper soil layer was more susceptible to changes in the pore size distributions due to the formation of new elongated pores. We concluded that this specific structural porosity was related to the decomposition of organic matter during the formation of soil aggregates.