Habitat features associated with species niches are commonly used as biodiversity proxies. Such proxies usually describe habitat diversity and have seldom been evaluated in a forestry context. As demands on forests to mitigate climate change and biodiversity loss increase, Conservation Value Assessments (CVAs) based on habitat diversity are increasingly utilised to guide conservation and resource extraction decisions. In central Sweden, we investigated the effectiveness of two widely used CVA protocols that assess forest habitat diversity to determine their ability to predict the occurrence of red-listed species for conservation prioritisation. We found that the tested CVAs effectively predicted the occurrence of red-listed wood-inhabiting bryophytes and fungi but were less effective for epiphytic and epixylic lichens or for predicting the occurrence of red-listed species across these three taxo-ecological groups. For red-listed bryophytes and fungi, we were able to identify ecological transition points where the probability of species occurrence had its most rapid increase. In addition, we identified threshold values above which the probability of finding one red-listed species was higher than not finding any red-listed species. These findings define conservation priority zones, which can guide prioritisation and restoration targets. Moreover, our study clearly shows that sites occupied by red-listed species had higher local species richness of non red-listed species in the same organism group. In conclusion, CVAs based on habitat diversity are valuable for identifying and prioritising areas for conservation of certain taxo-ecological groups, broader biodiversity assessments require complementary approaches to encompass the full taxo-ecological diversity in forests.