Healthy, resilient, and diverse marine ecosystems are capable of generating the biotic and abiotic components of natural capital stocks interacting and providing a bundle of ecosystem services vital to human well-being. Increasing pressures and impacts of human activities on marine ecosystems cause habitat degradation and biodiversity loss, and, as a consequence, seriously affect their capacity to provide benefits to humans. Integrated approaches capable of combining ecological and socioeconomic aspects are much needed to protect natural capital stocks and ensure the delivery of ecosystem services. In this context, marine protected areas (MPAs) are important tools for conserving biodiversity while promoting sustainable human activities. In this study, an interdisciplinary approach to the assessment of natural capital and ecosystem services in marine ecosystems was adopted. In particular, the emergy and eco-exergy accounting methods were jointly used to account for the biophysical value of natural capital stocks in the Mediterranean MPA “Punta Campanella”, located in Southern Italy. The assessment focused on four main macro-habitats: sciaphilic hard bottom (coralligenous bioconstructions), photophilic hard bottom, soft bottom, and Posidonia oceanica seagrass beds. The habitat Posidonia oceanica seagrass beds showed the highest value of eco-exergy density (3.58∙106 kJ m−2) while the highest value of emergy density resulted for the sciaphilic hard bottom habitat (4.94∙1012 sej m−2). The high eco-exergy value of Posidonia oceanica seagrass beds habitat is mainly due to the complex evolutionary history and high biomass density of the Posidonia oceanica seagrass. On the other hand, the high emergy value calculated for the sciaphilic hard bottom habitat reflects the high convergence of natural input flows for the generation of its biomass stocks and high biodiversity. In addition, to complement the biophysical assessment with an economic perspective, the emergy values of natural capital stocks were also converted into monetary units. The total value of natural capital stocks in the MPA resulted about 12 M€. Furthermore, a set of ecosystem services generated by Posidonia oceanica seagrass beds and Coralligenous bioconstructions was identified and their economic value was estimated (3.05 M€ and 0.62 M€, respectively). Finally, the value of natural capital and ecosystem services was also estimated by using a 3D bionomic map to consider the presence of Coralligenous bioconstructions and other habitats on cliffs characterizing the investigated MPA. This study highlighted the importance of Posidonia oceanica seagrass beds and Coralligenous bioconstructions in terms of both natural capital stocks and delivery of ecosystem services, confirming the need for their protection and conservation in marine and coastal management. The biophysical and economic values of natural capital stocks and ecosystem services, together with their spatial distribution in the MPA, can support local managers and policy makers in implementing and developing nature conservation strategies while ensuring the sustainable use of marine resources.