Earth’s most complex and biodiverse ecosystems are characterised by high habitat complexity. On coral reefs, habitat complexity is influenced by the diverse morphology and composition of hard corals, shaping reef structure and shelter provision for many species. Various metrics are used to quantify reef complexity, yet it remains unclear how well metrics capture ecological functions such as shelter provision. The diversity of coral communities means there is no ‘one metric fits all’ solution. We used a published dataset of 13 distinct coral community types generated using a 3D functional-structural model, to investigate the redundancy, complementarity and ecological relevance of 11 habitat complexity metrics (four general structural and seven ecologically meaningful shelter metrics). We were especially interested in the extent to which structural metrics can predict shelter metrics, potentially reducing the need for more complicated direct shelter measurements. We used Pearson’s correlations to compare metrics in (i) one pooled analysis from all community types, and (ii) 13 individual analyses for each community type. In the pooled analysis, structural metrics were strongly correlated while the shelter metrics formed two distinct groups – ‘pelagic’ and ‘benthic’ – where the metrics were highly correlated (i.e. redundant) within the groups but showed weak correlations between (complementary). Certain coral morphologies influenced the redundancy or complementarity of these metrics, where structural metrics can be useful predictors of shelter metrics when community type is known: e.g. surface rugosity was a stronger predictor of shelter volume, particularly for tabular and digitate coral communities. Fractal dimension was highly complementary to other metrics, but further investigation is needed to identify its ecological relevance. We highlight that there is no universal metric, and it is important to consider a range of suitable habitat complexity metrics and morphological community composition with our findings also relevant to ecosystems with morphologically distinct biogenic habitat formers.