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Protected areas are recognized as a crucial tool to mitigate ongoing trends of biodiversity loss. The effect of different levels of protection and their subsequent conservation efficiency remains, however, largely unexplored. To fill this gap, we present here an integrated approach that combines taxonomic analysis based on typical species to evaluate habitat quality and functional analysis based on plant traits to define habitat structure and functions. We focused on shrubland habitats across levels of protection in two different biogeographical areas. We found that habitat quality does not change linearly with levels of protection. Furthermore, the increase in habitat quality is characterized by a homogenization of habitat structure and functions, mostly driven by an increase in typical species. Our study suggests the level of protection afforded by protected areas is not necessarily indicative of their quality. A combined taxonomic and functional approach in protected areas can offer a thorough appraisal of habitat quality. • We assessed habitat quality in protected areas (PAs). • We tested it using typical species and functional traits. • We found different results in two biogeographically contrasting study areas. • Protection level of PAs is not a good predictor for habitat quality. • Combination of typical species and plant traits is recommended for PAs appraisal. [ABSTRACT FROM AUTHOR]