One of the most important pieces of climate change evidence is ocean acidification. Acidification effects on marine organisms are widely studied, while very little is known regarding its effects on assemblages’ β-diversity. In this framework, shallow hydrothermal vents within a Marine Protected Area (MPA) represent natural ecosystems acting as laboratory set-ups where the continuous carbon dioxide emissions affect assemblages with consequences that can be reasonably comparable to the effects of global water acidification. The aim of the present study is to test the impact of seawater acidification on the β-diversity of soft-bottom assemblages in a shallow vent field located in the Underwater Archeological Park of Baia MPA (Gulf of Naples, Mediterranean Sea). We investigated macro- and meiofauna communities of the ‘Secca delle fumose’ vent system in sites characterized by sulfurous (G) and carbon dioxide emissions (H) that are compared with control/inactive sites (CN and CS). Statistical analyses were performed on the most represented macrobenthic (Mollusca, Polychaeta, and Crustacea), and meiobenthic (Nematoda) taxa. Results show that the lowest synecological values are detected at H and, to a lesser extent, at G. Multivariate analyses show significant differences between hydrothermal vents (G, H) and control/inactive sites; the highest small-scale heterogeneities (measure of β-diversity) are detected at sites H and G and are mainly affected by pH, TOC (Total Organic Carbon), and cations concentrations. Such findings are probably related to acidification effects, since MPA excludes anthropic impacts. In particular, acidification markedly affects β-diversity and an increase in heterogeneity among sample replicates coupled to a decrease in number of taxa is an indicator of redundancy loss and, thus, of resilience capacity. The survival is assured to either tolerant species or those opportunistic taxa that can find good environmental conditions among gravels of sand.