Coralligenous bioconstructions are priority habitats crucial for the protection of Mediterranean marine biodiversity. Among these bioconstructions, the mesophotic biogenic reefs of the northern Adriatic are of particular concern due to their ecological relevance and the high levels of human pressure in the region. Thus, effective monitoring strategies are vital for the conservation and management of these fragile environments. In this study, we investigated the multivariate spatial and temporal patterns of sessile macrobenthos on biogenic reefs within two areas of a Natura 2000 site in the northern Adriatic over a four-year period. We also classified the ecological status of reefs based on the NAMBER index, specifically tailored for these peculiar bioconstructions. Our findings revealed that temporal trajectories of assemblages significantly differed between the two investigated areas, mostly due to larger fluctuations in algal turf abundance in the area closest to the coast, which is putatively more exposed to human impacts. In this area, the index identified a “Moderate” status during the period of peaking turf abundance, while the reef status consistently remained “Good” in other periods and in the area located further from the coast. This highlights the index sensitivity in reflecting actual changes in assemblages potentially associated with reef degradation.