Climatic changes can affect species distributions, population abundance, and evolution. Such organismal responses could be determined by the amount and quality of available habitats, which can vary independently. In this study, we assessed changes in habitat quantity and quality independently to generate explicit predictions of the species’ responses since the Last Glacial Maximum (LGM) climatic changes. We built ecological niche models and distribution models for 21 reptile, mammal, and plant taxa from the Baja California peninsula inhabiting lowland or highland environments. Geological data suggests the CCSM global circulation model is a better representation of LGM climate for the Baja California peninsula. Significant niche divergence was detected for all clades within species, along with significant differences in niche breadth and area of distribution between northern and southern clades. Most clades showed a reduction in distribution area towards LGM. Further, niche marginality (used as a measure of habitat quality) was higher during LGM for most clades, except for northern highland species who experienced improvements in both. Our results suggest that changes in habitat quantity and quality can affect organismal response independently. This allows the prediction of genomic signatures associated with changes in effective population size and selection pressure that could be explicitly tested to support our models.