The main objective of the present paper is to show and analyse major methodological challenges faced by the economic theory of the firm which, in turn, attempts to describe and explain transition processes in post-socialist economies. The economic theory of the firm is still faced by important challenges. The methodological weaknesses of the theory are the cause of significant cognitive limitations in the field of the transitional processes of enterprises from post-socialist economies. Overcoming these weaknesses is a condition for making progress in research on the system changes considered on a microeconomic scale in the countries of Central and Eastern Europe.