Abandoned, lost or otherwise discarded fishing gear (ALDFG) represents a major source of disturbance for benthic habitats, causing mechanical damage, covering burrows and trapping mobile fauna. ALDFG removal is commonly considered a mitigation measure, but in structurally complex ecosystems such as Mediterranean coralligenous reefs it may involve ecological trade-offs. Old gear often becomes colonised with fragile, long-lived benthic species, making removal a potential source of further environmental damage. This study investigates whether a gear-based removal-priority index is consistent with a habitat ecological status index, and whether integrating the two can inform selective removal decisions. The coralligenous reefs affected by ALDFG at Santo Stefano al Mare (Ligurian Sea) were investigated within the PNRR-MER-Ghost Nets-M2 C4 I3.5 “Ripristino e tutela dei fondali e degli habitat marini” project. Multibeam Echo Sounder, Side Scan Sonar and Remotely Operated Vehicle surveys enabled seabed characterisation, gear georeferencing and visual assessment of associated benthic communities. Fifteen ALDFG items were recorded on mobile bottoms, rocky outcrops and coralligenous reefs. For each gear, the Removal Aid Index (RAI) was calculated to estimate removal priority by integrating environmental impact, seascape impact and technical risk. Habitat ecological status was assessed within gear-impacted sites, applying COralligenous Assessment by Reef Scape Estimate (COARSE) index to the basal, intermediate and upper layers. Results show that all recorded gears were classified as low or non-urgent removal priority according to RAI. COARSE indicated an overall good ecological status, reflecting the good status of the basal and upper layers, while the intermediate layer showed a moderate ecological status. This suggests consistency between RAI and COARSE. Nevertheless, the lower ecological status of the intermediate layer highlights layer-specific variability in the coralligenous assemblage, supporting COARSE as an ecological complement to gear-based assessments. Comparing the two indices may therefore strengthen ALDFG removal decision-making and support habitat-sensitive management.