Sustainable Development Goals (SDGs). This has prompted calls for less use of mineral fertilizer and greater reliance on organic fertilizers. However, we need to understand better the long-term effects of organic fertilizer usage on soil structure to guide soil management practice, as many soil functions are sensitive to pore morphology and connectivity. In this study, we characterized topsoil (0–30 cm) pore architecture in relation to soil physical properties in a long-term experiment (LTE) site where calcareous soil had received 25 years of sewage sludge application. Two dosage rates (SSa, 20 and SSe, 80 Mg ha−1) were compared to mineral fertilization treatment and a control (no fertilization) in a random factorial block design. Soil microstructure and the types of pores were characterized using micromorphological methods and image analysis, in soil thin sections. Long-term sewage sludge SSa application improved soil microstructure (crumb and sub-angular-blocky type) and increased the presence of biopores, while mineral fertilized soil showed a platy to apedal microstructure, with more elongated pores and lower faunal activity. Mineral fertilized soil had the lowest total porosity values, with differences found in the aspect ratio of pores of equivalent diameter 100–200 μm. These findings suggest a relation between the different types of fertilization and soil pore shape and network. Further exploration of these changes in soil functioning is needed for a complete assessment of the consequences of SS application.