The study is part of the trend of searching for research methods to demonstrate changes in forest cover at the level of basic units of public administration with greater precision and accuracy. The purpose of the article is to present, for the first time, changes in forest cover of municipalities in Poland from 1990 to 2018 using CORINE Land Cover (CLC) data. The contributions of this study are threefold. Firstly, using GIS and CLC data (3.1. Forests), multivariate analyses of forest cover changes were carried out for 2481 municipalities for the CLC data collection years (1990, 2000, 2006, 2012, 2018), which showed the temporal and spatial dynamics of changes, with a predominance of deforestation in 1990–2000 and 2012–2018, and afforestation in 2000–2006 and 2006–2012. Secondly, the formal, legal and financial rationale for these changes was indicated. The increase in afforestation was a result of financial incentives under the National Program for Increasing Forest Cover and the EU’s Common Agricultural Policy (under Rural Development Programs—RDPs). Deforestation was related to a decrease in the supply of land for afforestation, the competitiveness of subsidies implemented under RDPs, and statutory liberalization of logging. Thirdly, the main discrepancies between the data obtained from CLC and from the public data collected by Statistics Poland (GUS) and the State Forests were indicated, which ranged from −32 kha to +310 kha, corresponding to percentage differences of 2.3% and 1.8%, respectively. This was mainly influenced by the differences in the complexity and updating of data collected for state and private forests, as well as delays in introducing changes to the land register by the public administration. This work contributes significantly to our understanding of the dynamics of forest cover changes in relation to the actual degree of forestation and deforestation, and the determinants of forest transformation in Polish municipalities, as well as demonstrating the new applicability of CLC data and their limitations related mainly to the generalization of forest cover area.