Currently, most European Union member states have established their maritime spatial plans as mandated by the Maritime Spatial Planning Directive (Directive 2014/89/EU). This directive establishes that an ecosystem-based approach (EBA) must be followed when developing national plans, yet it lacks practical guidance on its implementation. While various approaches to ecosystem-based marine spatial planning (EB-MSP) have been proposed in the scientific literature, a standardised framework for integrating EBA principles into MSP remains elusive, resulting in considerable variability among existing MSPs. Consequently, it is particularly pertinent at this time to evaluate current national plans for their adherence to ecosystem-based management principles, to identify the strengths and weaknesses of existing plans and to provide guidance for the effective implementation of EB-MSP in future revisions of plans within European Seas. All work carried out in WP1 has focused on operationalising EB-MSP and developing a best practice guide for its implementation in European Seas. Framing and operationalising EB-MSP (T1.1) involved the development of the EB-MSP framework and its operationalisation as a decision support system (DSS), intended for testing and implementation by Planning Sites. The EB-MSP process template was conceptualised to be applicable across the European Seas and beyond, and therefore, it seeks to advise on the general linkages between environmental, economic and social attributes of a marine system in the light of climate change. Supported by WP4 and WP5, WP1 of MarinePlan liaised with key stakeholders to inform the underlying concepts and scientific knowledge base during the operationalisation of the EB-MSP framework (M1.1) and the definition of operational objectives for EB-MSP (M1.2). The requirements and recommendations from stakeholders were considered when developing a realistic and applicable EB-MSP process template. The EB-MSP process template considers the relationship between humans and the marine ecosystem (T1.2), recognising humans as both beneficiaries of ecosystem services and contributors to negative effects on environmental and conservation status. Hence, the EB-MSP process template addresses cause-effect pathways (M1.3) and cumulative effects assessments (CEA), which are crucial for the spatial planning of marine activities while aiming to safeguard biodiversity. Upon the development of the EB-MSP process template (D1.1), a workshop was conducted with Planning Sites leaders to ensure a common understanding of concepts and to guide its implementation in a comparable way (M1.4). The EB-MSP process template was operationalised into an EB-MSP assessment tool (https://aztidata.es/EB-MSP/), an open-access web application. This tool addresses the implementation challenges of ecosystem-based management principles in MSP processes. It considers specific actions that should be addressed throughout the planning process, providing a structured assessment method for practitioners and competent authorities to ensure coherent and transparent planning. As the EB-MSP implementation process aims to be “product-oriented” with maximum utility for both scientists and managers (M1.5), standardised feedback on implementation experiences was collected to improve subsequent versions of the EB-MSP process template. The recommendations obtained informed the development of this best practice guidance (D1.2), which provides the means to effectively align marine conservation planning with MSP and offers a basis for monitoring and evaluating EB-MSP outcomes.