The Mediterranean Sea is undergoing ecological degradation driven by overfishing and other anthropogenic stressors, which, together with climate change, lead to the loss of upper-trophic-level biodiversity and affect ecosystem functioning. Marine Protected Areas (MPAs) are widely used to mitigate the direct impacts and support marine biodiversity conservation. However, total fish biomass, one of the most commonly used metrics, does not explicitly quantify how biomass is distributed across trophic levels. Understanding how fish trophic structure changes over time, therefore, remains key to evaluating the effectiveness of protection measures. In this study, we applied the Normalized Reef Status Index (NRSI) to the Mediterranean context for the first time to assess how the trophic structure of rocky reef fish assemblages varied over time across different protection levels. We compared fish biomass across low, intermediate, and high trophic levels among fully protected, partially protected, and unprotected areas over the long-term period (2007–2025) in the Tavolara – Punta Coda Cavallo MPA (Sardinia, Italy). A clear gradient among protection levels was detected since the beginning of the study period, that persisted through years. The fully protected area showed positive NRSI values, indicating a greater contribution of upper trophic-level species to total biomass. In contrast, the partially protected areas remained close to zero, while the unprotected area showed mostly negative values. Beta regression confirmed a strong positive effect of protection on the NRSI, with both fully and partially protected areas showing significantly higher values than the unprotected area. The model also revealed a small but significant negative effect of year, reflecting a mild overall decline shared across all protection levels. Despite this slight common decline, the NRSI did not follow a consistent directional trend but fluctuated over time within each protection level. In the fully protected area, an initial decline was followed by stabilization at positive values, indicating the persistence of a predator-oriented structure. Importantly, differences among protection levels persisted throughout the study period. Overall, our findings indicate that protection exerted a consistent positive effect on reef fish trophic structure over time, and that the NRSI provides a standardized and scalable framework for detecting and tracking differences in trophic structure across protection levels.