We analyze the effect of Robin boundary conditions in a mathematical model for a mitochondria swelling in a living organism. This is a coupled PDE/ODE model for the dependent variables calcium ion contration and three fractions of mitochondria that are distinguished by their state of swelling activity. The model assumes that the boundary is a permeable 'membrane', through which calcium ions can both enter or leave the cell. Under biologically relevant assumptions on the data, we prove the well-posedness of solutions of the model and study the asymptotic behavior of its solutions. We augment the analysis of the model with computer simulations that illustrate the theoretically obtained results.