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Given the magnitude and rate of ongoing climate change, the physiological capacity of species to tolerate extreme conditions will play a key role in influencing outcomes for biodiversity. It is also possible that species will respond to changes in climate by shifting their physiological tolerances, through genetic adaptation. How these processes influence biodiversity outcomes will be crucial in determining the most suitable management responses to retain diversity into the future. Here we assess how accounting for physiological tolerances, genetic adaptation and community assembly processes such as species replacement, influence projected climate change outcomes for the flora of Tasmania (all 2051 plant species). We incorporate these processes into the M-SET metacommunity model and compare four different assumptions of species niches: realized niches, broader physiological tolerances and low or high capacity for genetic adaptation. Accounting for physiological tolerances rather than realized niches had the largest impact on projected outcomes, with 358 fewer species extinctions in the hottest climate scenario (mean = 30 extinctions). In contrast, adding the capacity for species physiological tolerances to shift through genetic adaptation resulted in little additional benefits for biodiversity outcomes, even under an optimistic level of adaptive capacity. We find that this is due largely to community assembly processes such as species replacement restricting the ability of species to persist and adapt in situ, as has been suggested from theoretical metacommunity models applied in simple artificial settings. Our results highlight the importance of accounting for species physiological tolerances and community-level processes in biodiversity projections, while the potential role for genetic adaptation may be small, requiring further exploration in alternative contexts.