Habitat loss is widely considered the greatest threat to biodiversity. However, habitat loss brings with it myriad other threats that exacerbate impacts to biodiversity. For instance, altered fire regime is associated with habitat loss and fragmentation with unknown consequences to biodiversity. Plant functional groups that rely on fire to complete their life cycle may be adversely affected by disruptions to the natural fire regime, particularly when coupled with population declines due to habitat loss. We used a spatially explicit stochastic population model linked with fire hazard functions to investigate the cumulative effects of habitat loss, fragmentation, and altered fire regime on the expected minimum abundance of a long-lived obligate-seeding shrub, Ceanothus greggii var. perplexans. This species is endemic to the California Floristic Province, a biodiversity hotspot, and is representative of a functional group of plants found in many fire-prone ecosystems. We tested the impact of a range of different fire frequencies under three different combinations of fuel accumulation and weather. The best average fire return interval for population abundance was consistently in the range of 30-50 years. However, observed average fire return intervals in highly fragmented areas can be approximately 20 years or less, and model results show this to be detrimental to C. greggii populations. Results also show that if fires are uncorrelated across habitat fragments then the impact of altered fire regime on populations is worse than the impact of habitat fragmentation because of spatial and temporal decoupling of fire events across the landscape. However, the negative impacts of altered fire regime are outweighed by habitat loss as fragmentation increases. Our results show that large unplanned fires, operating under an altered fire regime, are ultimately detrimental to perennial obligate-seeding shrubs in fragmented landscapes.