Aim Species respond to environmental conditions and so reliable assessments of climate suitability are important for predicting how climate change could alter their distributions. Long‐term average climate data are often used to evaluate the climate suitability of an area, but in these aggregated climate datasets, inter‐annual variability is lost. Due to non‐linearity in species’ biological responses to climate, estimates of long‐term climate suitability from average climate data may be biased and so differ from estimates derived from the average annual suitability over the same period (average response). We investigate the extent to which such differences manifest in a regional assessment of climate suitability for 255 plant species across two 17‐year time periods. Location Cornwall in South‐West England provides a case study. Taxon Plantae. Methods We run a simple mechanistic climate suitability model and derive quantitative estimates of climate suitability for 1984–2000 and 2001–2017. For each period, we run the model using climate data representing average monthly values for that period. We then run the model for each year using monthly climate data for that year and average the annual suitability scores across each period (average response). We compare estimates of climate suitability from these two approaches. Results Average climate data gave higher estimates of suitability than the average response, suggesting bias against years of poor suitability in temporally aggregated climate datasets. Differences between suitability estimates were larger in areas of high climate variability and correlated with species’ environmental requirements, being larger for species with small thermal niches and narrow ranges of precipitation tolerance. Main Conclusions Incorporating inter‐annual variability into climate suitability assessments or understanding the extent to which average climate data might obscure this variance will be important to predict reliably the impacts of climate change on species distributions and should be considered when using mechanistic species distribution models.