Abstract Macroalgal forests, such as Cystoseira sensu lato, comprise crucially important habitats in the Mediterranean Sea, providing protection and structural complexity, enhancing productivity, food, shelter and spawning grounds in coastal marine ecosystems. However, due to increasing direct and indirect anthropogenic impacts, these habitats are rapidly declining. Due to their biological and ecological characteristics, the natural recovery of the populations belonging to these species is slow. For this reason, active restoration has been identified as an effective tool for their recovery. Since the mitigation of impacts is one of the prerequisites for restoration success, Modified Threat Reduction Assessments were used to estimate success of conservation measures in three areas of the central and north‐western Mediterranean Sea (Costa del Conero, Italy; Cala Bona and Port de la Selva, Spain). In particular, the assessment was conducted to: (i) identify and evaluate the changes in threats to Cystoseira s.l. species between 2019 and 2021; and (ii) propose management in relation to the ongoing restoration measures. A total of 13 threats were identified and determined negative Modified Threat Reduction Assessment Indices of approximately −46%, −14% and −13%, respectively, in Costa del Conero, Cala Bona and Port de la Selva. The study's findings, when combined, document the increase of the scale of threats during the second year of the survey period despite the lockdown due to COVID‐19.