Changing climate and disturbance regimes are increasingly challenging the resilience of forest ecosystems around the globe. A powerful indicator for the loss of resilience is regeneration failure, that is, the inability of the prevailing tree species to regenerate after disturbance. Regeneration failure can result from the interplay among disturbance changes (e.g., larger and more frequent fires), altered climate conditions (e.g., increased drought), and functional traits (e.g., method of seed dispersal). This complexity makes projections of regeneration failure challenging. Here we applied a novel simulation approach assimilating data-driven fire projections with vegetation responses from process modeling by means of deep neural networks. We (i) quantified the future probability of regeneration failure; (ii) identified spatial hotspots of regeneration failure; and (iii) assessed how current forest types differ in their ability to regenerate under future climate and fire. We focused on the Greater Yellowstone Ecosystem (2.9 × 106 ha of forest) in the Rocky Mountains of the USA, which has experienced large wildfires in the past and is expected to undergo drastic changes in climate and fire in the future. We simulated four climate scenarios until 2100 at a fine spatial grain (100 m). Both wildfire activity and unstocked forest area increased substantially throughout the 21st century in all simulated scenarios. By 2100, between 28% and 59% of the forested area failed to regenerate, indicating considerable loss of resilience. Areas disproportionally at risk occurred where fires are not constrained by topography and in valleys aligned with predominant winds. High-elevation forest types not adapted to fire (i.e., Picea engelmannii–Abies lasiocarpa as well as non-serotinous Pinus contorta var. latifolia forests) were especially vulnerable to regeneration failure. We conclude that changing climate and fire could exceed the resilience of forests in a substantial portion of Greater Yellowstone, with profound implications for carbon, biodiversity, and recreation.