Background: Prescribed fire is increasingly used to accomplish management goals in fire-adapted systems, yet our understanding of effects on non-target organisms remains underdeveloped. Terricolous lichens in the genus Cladonia P. Browne, particularly cushion-forming reindeer lichens belonging to Cladonia subgenus Cladina Nyl., fit into this category, being characteristic of fire-adapted ecosystems, yet highly vulnerable to damage or consumption during burns. Moreover, inherently slow dispersal and growth rates raise questions about how to conserve these taxa in the context of fire-mediated restoration management. This research was undertaken to identify factors that contribute to Cladonia persistence within areas subject to repeated burning and involved tracking the fate of 228 spatially isolated individuals distributed across seven sites previously burned zero to two times. Site selection was determined by edaphic factors associated with a rare inland dune woodland community type known to support relatively high densities of Cladonia. Results: Evaluated across all sites, the post-burn condition of Cladonia subtenuis (Abbayes) Mattick samples, categorized as intact (32%), fragmented (33%), or consumed (36%) individuals, approximated a uniform distribution. However, their status was highly variable at the different sites, where from 0 to 70% were assessed as intact and 11 to 60% consumed. Machine-learning statistical techniques were used to identify the factors most strongly associated with fire damage, drawing from variables describing the proximate fuel bed, growth substrate, and fire weather. The final descriptive model was dominated by variables characterizing the understory fuel matrix. Conclusions: Areas with highly contiguous fuels dominated by pyrogenic pine needles were most likely to result in consumption of individual Cladonia, whereas those growing in areas with low fuel continuity or in areas dominated by hardwood litter were more likely to persist (intact or as fragments). Further, substrates including bare soil and moss mats afforded more protection than coarse woody debris or leaf litter in settings where fuels were both contiguous and highly flammable. Our findings describe the characteristics of within-site fire refugia, the abundance of which may be enhanced over time through restoration and maintenance treatments including thinning, promotion of mixed-species overstory composition, and periodic burning. Because lichens contribute to, and are considered reliable indicators of forest health, fire-based restoration management efforts will benefit from improved understanding of how these vulnerable organisms are able to persist.