Tissue engineering is a fast progressing domain where solutions are provided for organ failure or tissue damage. In this domain, computer models can facilitate the design of optimal production process conditions leading to robust and economically viable products. In this study, we use a previously published computationally efficient model, describing the neotissue growth (cells + their extracellular matrix) inside 3D scaffolds in a perfusion bioreactor. In order to find the most cost-effective medium refreshment strategy for the bioreactor culture, a multi-objective optimization strategy was developed aimed at maximizing the neotissue growth while minimizing the total cost of the experiment. Four evolutionary optimization algorithms (NSGAII, MOPSO, MOEA/D and GDEIII) were applied to the problem and the Pareto frontier was computed in all methods. All algorithms led to a similar outcome, albeit with different convergence speeds. The simulation results indicated that, given the actual cost of the labor compared to the medium cost, the most cost-efficient way of refreshing the medium was obtained by minimizing the refreshment frequency and maximizing the refreshment amount.