Muscari gussonei is an endangered endemic plant growing on fragmented Mediterranean coastal dunes. This study focused on the germination performance of M. gussonei at two fixed temperatures, 10 and 15 °C, and at an alternating one, 10/20 °C, and on the multi-temporal trends of temperature and rainfall during 1931–2020, as well as on the patterns of desertification and land-cover changes over the last 60 years. High and similar germinability was found for different populations of M. gussonei, in particular, the final germination percentage (FGP) was ≥95 % for the three treatments. The general pattern was the lower the temperature the higher and faster the germination. However, germination speed varied significantly among populations. This intraspecific variability of germination behavior may suggest a certain level of ecophysiological plasticity in M. gussonei, thus raising hopes on the capacity of M. gussonei to respond better to the ongoing severe environmental changes. In the period 1931–2020, indeed, the average temperature rose by 1.5 °C, from 16.8 to 18.3 °C, which is equivalent to the enormous increase of 0.17 °C per decade. Similarly, the average rainfall declined by 100 mm, from 600 to 500 mm. Another serious stressor was desertification, which affects >90 % of the distributional area of M. gussonei. A further factor of ecological degradation is a considerably altered landscape, where the agricultural component accounts for c. 85 %, whereas natural and seminatural areas were only c. 10 %. Increasing temperature and dryness will inevitably reduce the germinability of M. gussonei, characterized by a narrow germination optimum of 10–15 °C. The future of M. gussonei looks even more dramatic if we consider its small and scattered populations distributed in an agricultural matrix affected by high levels of desertification. Only multivariate information at different space-time scales can provide an exhaustive picture for implementing effective conservation strategies.