This paper presents the process of advanced numerical analysis of interaction between a building and the subsoil. The analysis covered a wide range of work for both computing and research. As part of the research work, field and laboratory subsoil tests were carried out, as well as geodetic measurements of building settlement and measurements of natural vibrations of an object. The computational work included the analysis of a total of 47 FEM models. The subsoil was described using the Modified Cam-Clay model, with parameters determined using field CPT and SDMT tests, as well as triaxial and edometric laboratory tests. Parts with geodetic benchmarks were separated from the building model, and then multi-variant calculations were made on smaller, partial models with parameters obtained from various methods. Calibration of the main models was performed using 8 partial models for which calculations were carried out in 4–5 variants of parameters. This gave a total of 38 partial models. Then, calculations were carried out on the full model of the building with subsoil. At each stage, the results of vertical displacements were compared to the geodetic values. The measured settlement of the real building in the time from the construction of the underground story to its use for the period of 1 year, was from 2.3 mm to 7.8 mm. The settlement from FEM calculations of small calibration models for the same benchmarks was from 2.0 mm to 9.8 mm with parameters derived from CPT tests and from 1.8 to 7.3 mm for parameters derived from SDMT. For the full building model, settlement from FEM calculations ranged from 2.2 to 8.8 for the variant with a simplified subsoil model, and from 3.7 to 10.5 for the model taking into account the inhomogeneity of the subsoil. As a result, it was found that the displacements from the numerical analysis were convergent with the geodetic values. Detailed numerical analyses also allowed to detect the deviations of the segments from the vertical and to indicate potential damage to the structure. It was also indicated how the work of the subsoil influences the stress distribution in selected structural elements. Behaviour of the subsoil has an impact on the behaviour of the building and its deformations, as well as on the distribution of stresses in the structural elements, and, as a result, on the change in the distribution of internal forces in the structure.