The human gut microbiome exhibits characteristics of complex ecosystems, including the ability to resist and compete with exogenous species or communities. Understanding microbiome responses to such competition is crucial, especially for fecal microbiota transplantation (FMT), where success depends on microbial interactions. During these processes, microbial communities undergo coalescence, combining and interacting in ways that lead to complex ecological outcomes. In this study, we investigated the coalescent dynamics of ten pairs of human gut microbiota through in vitro co-culturing. Metaproteomic analysis revealed that post-coalescence changes were not simply an average of the initial microbiotas but instead, both coalescent microbiotas behaved as cohesive structures, influencing the competitive outcome towards one of them. While taxonomic similarities were observed between co-cultured communities and their parental samples, 23% of proteins showed differential expression. Interestingly, the competitive outcomes followed a “rock-paper-scissors” dynamic, with different species contributing to competition outcomes across different pairs. This highlights the complexity of microbial competition, suggesting that no single factor consistently determines dominance. Pre-co-culturing may thus be a promising method for predicting outcomes in FMT and other ecological therapies.