The prevailing method for estimating the potential impact of future climate change on biological communities is to stack binary predictions from species distribution models (binary stacked species distribution models, bS-SDM). However, it has been argued that bS-SDM may overestimate species richness and, hence, community composition. Alternative approaches, such as SESAM (‘Spatially Explicit Species Assemblage Modelling’), explicitly incorporate limits to species richness, preventing overestimation. We compared richness and taxonomic composition estimates as predicted by SESAM and bS-SDM for Mediterranean bird communities both in the present day and as projected in the future under simulated climate change scenarios. We trained single-species distribution models (S-SDM) and direct macroecological richness models (MEM) for 81 bird species using climate, topographic, land-use and human-pressure indicators as predictors. We then evaluated and compared model predictions. Species richness as predicted by bS-SDM was more accurate than under SESAM for present-day communities. Taxonomic composition was well predicted under both methods. However, we detected significant differences in future projections. Under bS-SDM, increased suitable area for a number of species leads to important changes in community composition and predicts higher levels of diversity in the future. In stark contrast, SESAM predicts lower species richness in the future and strong homogenization of bird communities across space. This study shows how the choice of the modelling approach drives substantially different expectations about future community composition under climate change. We therefore recommend contrasting predictions generated under different modelling approaches to gain better understanding of possible future scenario of biodiversity change.