Gopher Tortoise (Gopherus polyphemus) burrows support diverse commensal invertebrate communities that may be of special conservation interest. We investigated the impact of red imported fire ants (Solenopsis invicta) on the invertebrate burrow community at 10 study sites in southern Mississippi, sampling burrows (1998–2000) before and after bait treatments to reduce fire ant populations. We sampled invertebrates using an ant bait attractant for ants and burrow vacuums for the broader invertebrate community and calculated fire ant abundance, invertebrate abundance, species richness, and species diversity. Fire ant abundance in gopher tortoise burrows was reduced by >98% in treated sites. There was a positive treatment effect on invertebrate abundance, diversity, and species richness from burrow vacuum sampling which was not observed in ant sampling from burrow baits. Management of fire ants around burrows may benefit both threatened gopher tortoises by reducing potential fire ant predation on hatchlings, as well as the diverse burrow invertebrate community. Fire-ant management may also benefit other species utilizing tortoise burrows, such as the endangered Dusky Gopher Frog and Schaus swallowtail butterfly. This has implications for more effective biodiversity conservation via targeted control of the invasive fire ant at gopher tortoise burrows.