Monitoring of land cover plays an important role in effective environmental management, assessment of natural resources, environmental protection, urban planning and sustainable development. Increasing demand for accurate and repeatable information on land cover and land cover changes causes rapid development of the advanced, machine learning algorithms dedicated to land cover mapping using satellite images. Free and open access to Sentinel-2 data, characterized with high spatial and temporal resolution, increased the potential to map and to monitor land surface with high accuracy and frequency. Despite a considerable number of approaches towards land cover classification based on satellite data, there is still a challenge to clearly separate complex land cover classes, for example grasslands, arable land and wetlands. The aim of this study is to examine, whether a hierarchal classification of Sentinel-2 data can improve the accuracy of land cover mapping and delineation of complex land cover classes. The study is conducted in the Lodz Province, in central Poland. The pixel-based land cover classification is carried out using the machine learning Random Forest (RF) algorithm, based on a time series of Sentinel-2 imagery acquired in 2020. The following nine land cover classes are mapped: sealed surfaces, woodland broadleaved, woodland coniferous, shrubs, permanent herbaceous (grassy cover), periodically herbaceous (i.e., arable land), mosses, non-vegetated (bare soil) and water bodies. The land cover classification is conducted following two approaches: (1) flat, where all land cover classes are classified together, and (2) hierarchical, where the stratification is applied to first separate the most stable land cover classes and then classifying the most problematic once. The national databases served as the source of the reference sampling plots for the classification process. The process of selection and verification of the reference sampling plots is performed automatically. To assess the stability of the classification models the classification processes are performed iteratively. The results of this study confirmed that the hierarchical approach gave more accurate results compared to the commonly used flat approach. The median of the overall accuracy (OA) of the hierarchical classification was higher by 3–9 percentage points compared to the flat one. Of interest, the OA of the hierarchical classification reached 0.93–0.99, whereas the flat approach reached 0.90. Individual classes are also better classified in the hierarchical approach.