Planning a sustainable future for coastal populations requires the effective implementation of ecosystem management frameworks that explicitly incorporate human activities. A coupled framework of the Ecosystem-Based Approach with Marine Spatial Planning has been discussed and promoted by coastal managers for more than a decade. The proposed framework supports a balanced approach between development needs and the natural environment. This paper presents a qualitative review of Marine Spatial Planning case studies to gain insights into methodological approaches that account for human systems as components of the coastal environment. A total of twelve Marine Spatial Planning case studies were evaluated. Their use and integration of the Ecosystem-Based framework was assessed through a linguistic scale linked to a score of fuzzy numbers. Two management issues of interest were highlighted: how social, economic and environmental values were integrated into the spatial planning analysis; and how cross-realm connectivity was addressed by planning teams. Although the majority of case studies claimed to use the Ecosystem-Based Approach as the guiding framework, mixed results were observed. Relevant features of the Ecosystem-Based Approach were rarely included; such as the standardization of pressures from human activities, the integration of frameworks to assess ecosystem services and the implementation of Precautionary and Adaptive Management approaches. Important knowledge gaps were observed with regards to the assessment of social values, including the lack of spatial representation of ‘social connections’ to the marine environment and the lack of economic estimates of non-market values. Terrestrial and catchment units were not included in the majority of case studies; however, water quality management was used as a key element for the consideration of transboundary impacts. This comparative study reveals major differences in how coastal managers understand and integrate Ecosystem-Based Approaches with Marine Spatial Planning.