This Special Issue is a significant step in developing a new direction of metabolic research— Molecular System Bioenergetics, which itself is a part of Systems Biology. As a new paradigm of biological sciences, Systems Biology aims at understanding of biological functions by studies and description of new, system level properties, resulting from interactions between components of biological systems at any level of organization, from molecular to population. Metabolism is the way of life of cells by exchanging mass and energy with the surrounding medium, and understanding its mechanisms requires knowledge of the complex interactions between cellular systems and components. While studies of metabolism have a long history, new concepts of Systems Biology provide useful tools for metabolic research. According to Schrödinger, living cells need to be open systems with energy and mass exchange with the surrounding medium, with the aim of maintaining their high structural and functional organization and thus their internal entropy low, achieving this by means of increasing the entropy of the medium by catabolic reactions. Thus, Schrödinger wrote: “The essential thing in metabolism is that the organism succeeds in freeing itself from all entropy it cannot help producing while alive”. Thus, free energy conversion in the cells is an important, central part of metabolism, and understanding the complex mechanisms of its regulation is the aim of Molecular System Bioenergetics. In this Special Issue, several important problems in this field were analyzed.