Switching from the traditional 40- or 44-mm diamond mesh codends to 50-mm diamond mesh (D50) or 40-mm square mesh (S40) codends is known to improve the size selection for commercial species and reduce discarding in the Mediterranean demersal trawl fisheries. This change has been recommended in the General Fisheries Commission for the Mediterranean and European Commission regulations. However, ecosystem-based assessment of improved selectivity still remains a challenge, and that is the aim of this study. For this purpose, an Ecopath model was developed and used to initialize dynamic simulations in Ecosim. The simulations changed gear-specific fishing mortality rates to represent the shifting from traditional codend to alternative codends. Our results suggest that the use of D50 or S40 codends would have a positive impact on the ecosystem as a whole and on the stock status of several commercial and non-commercial groups. Mixed trophic impact analysis indicated that, for species, like red mullet, the S40 codend was significantly better than the D50 codend. This information can be useful to policymakers, particularly for the areas where red mullet is the main target species and could inform trawl mesh options in the eastern Mediterranean.