Entropy generation is one of the most decisive factors to determine the irreversibility characteristics of various heat transport processes. Therefore, this study explores the entropy generation caused by viscous dissipation, ohmic heating, mass transfers, and chemical reactions during Newtonian flow processes through a microchannel with ciliated walls. Mathematical framework of the present model is made up of five nonlinear partial differential equations in velocity components, pressure gradient, temperature, and concentration distributions. We scrutinize nonlinear system under the lubrication approximation theory and acquire a linear system of ordinary differential equations in a wave frame of reference. Exact analytical solutions for the velocity, pressure, temperature, and concentration distributions are constructed. Expressions for entropy production rate and Bejan number are also formulated for the present flow scenario. Effects of heat and mass transfers, Hartmann number, Hall current, chemical reaction, and the eccentricity parameter of ciliary beatings on the flow field, pumping characteristics, temperature, concentration, entropy production rate, and Bejan number are discussed in details. Outcomes of present model recommend that inclusion of Hall current overwhelms the damping effects of magnetic field and hence controls the irreversibility of thermodynamical systems. Moreover, in order to manipulate the flow and irreversibility in cilia-based micro-devices, the role of eccentricity parameter is noticeable. We hope that our theoretical results can be utilized in mixing and controlling various aspects of mass, momentum, and heat transfers in MHD-based microfluidic devices.