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Background: Systematic Conservation Planning (SCP) involves a series of steps to identify conservation areas and develop management strategies, incorporating feedbacks, revisions, and iterations at any stage. It is a valuable tool in facilitating the effective implementation of Ecosystem-Based Marine Spatial Planning (EB-MSP). However, few efforts have been carried out to summarize information on methods, trends, and progress in SCP in the designation of Marine Protected Areas (MPAs). The present work aims at providing the protocol to perform a scoping review (ScR) to assess the contribution of SCP to the design of effective MPA networks, identifying both the development of good practices and the presence of gaps of knowledge in terms of criteria for their implementation. Protocol: The ScR will follow the Joanna Briggs Institute (JBI) methodology. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) extension for ScRs supported the definition of this protocol. The three databases Web of Science, Scopus, and Google Scholar will be used for the bibliographic search. Inclusion criteria will be as follows: studies applying SCP in the marine realms worldwide, assessing its contribution to the design of MPA networks. Both peer-reviewed and grey literature will be considered for eligibility. No search limitations will be applied regarding publications’ year, stage, subject area and source type. Studies in English, French, German, Greek, Italian, and Spanish will be reviewed. Grey literature will be sourced from pre-print archives, institutional websites and other web-based search engines. The Covidence software will be used for the process of documents selection and data extraction. The findings of the ScR will be presented through tables, graphs, and maps, accompanied by a narrative summary of the outcomes. Conclusions: This comprehensive approach will provide a visual representation of the data, enhancing the understanding and interpretation of the results.