Cystoseira sensu lato marine forests, which are among the most productive and diverse systems in rocky intertidal and subtidal habitats of the Mediterranean Sea, are experiencing a widespread decline throughout the basin due to increasing human pressures. Yet it is still unclear whether Marine Protected Areas (MPAs) may represent effective tools for conservation of these important habitat formers and their associated assemblages. Here, we compared the biomass of intertidal stands of Ericaria amentacea (C. Agardh) Molinari and Guiry and their understory assemblages between the no-take zone and control sites in two Mediterranean MPAs. We did not find evidence supporting a significant effect of full protection in increasing the biomass of E. amentacea stands and associated assemblages, except for macroalgae of the understory in one of the investigated MPAs, raising concerns on the potential effectiveness of MPAs in mitigating human impacts on these marine forests. Such findings call for major efforts to implement long-term monitoring programs of protected Cystoseira s.l. forests in order to inform an adaptive management of conservation measures within MPAs and eventually to set active interventions of restoration.