The gut microbiota is known to influence and have regulatory effects in diverse physiological functions of host animals, but only recently has the relationship between host thermal biology and gut microbiota been explored. Here, we examined how early-life manipulations of the gut microbiota in larval amphibians influenced their critical thermal maximum (CTmax) at different acclimation temperatures. We removed the resident microbiome on the outside of wild-caught wood frog (Lithobates sylvaticus) egg masses via an antibiotic wash, and then either maintained eggs without a microbiota or inoculated eggs with pond water or the intestinal microbiota of another species, green frogs (L. clamitans), that have a wider thermal tolerance. We predicted that this cross-species transplant would improve the CTmax of the recipient wood frog larvae relative to the other treatments. In line with this prediction, green frog-recipient larvae had the highest CTmax while those with no inoculum had the lowest CTmax. Both the microbiome treatment and acclimation temperature significantly influenced the larval gut microbiota communities and alpha diversity indices. Green frog inoculated larvae were enriched in Rikenellaceae relative to the other treatments, which produce short-chain fatty acids and could contribute to greater energy availability and enhanced heat tolerance. Larvae that received no inoculation had higher relative abundances of potentially pathogenic Aeromonas spp., which negatively affects host health and performance. Our results are the first to show that cross-species gut microbiota transplants alter heat tolerance in a predictive manner. This finding has repercussions for the conservation of species that are threatened by climate change and demonstrates a need to further explore the mechanisms by which the gut microbiota modulates host thermal tolerance.