Habitat loss and population fragmentation pose severe threats to biodiversity and the survival of many species. Population isolation and the decline in effective population size lead to increased genetic drift and inbreeding. In turn, this reduces neutral diversity, and it also affects the genetic load of deleterious mutations. Here, we analyse the effect of such genomic erosion by designing a spatially explicit, individual based model in SLiM, simulating the effects of the recorded habitat loss in Mauritius over the past ~ 250 years. We show that the loss of neutral diversity (genome-wide heterozygosity) was barely noticeable during the first 100 years of habitat loss. Changes to the genetic load took even more time to register, and they only became apparent circa 200 years after the start of habitat decline. Although a considerable number of deleterious mutations were lost by drift, others increased in frequency. The masked load was thus converted into a realised load, which compromised individual fitness and population viability after much of the native habitat had been lost. Importantly, genomic erosion continued after the metapopulation had stabilised at low numbers. Our study shows that historic habitat loss can pose a sustained threat to populations also in future generations, even without further habitat loss. The UN’s Decade on Ecosystem Restoration needs to lead to transformative change to save species from future extinction, and this requires the urgent restoration of natural habitats.