In an era of unprecedented climatic variability, organisms must express flexible phenotypes to persist in thermally dynamic environments. Thermally-induced phenotypic plasticity may either promote or impair fitness, depending on the environment; however, the mechanisms underlying these phenotypic shifts are not well understood. Gut microbiota are shaped by the environment and have myriad effects on host phenotype. My dissertation investigates whether gut microbiota mediate coordinated phenotypic plasticity, primarily via experiments in tree swallows (Tachycineta bicolor), a declining bird species that is strongly impacted by fluctuations in environmental temperatures. One of the primary drivers of thermal plasticity is the glucocorticoid stress response, but individual differences in stress responsiveness may be indirectly driven by other physiological systems such as the gut microbiota. In Chapter 1, I reviewed the current evidence for and future applications of the gut microbiota as a mediator of stress responsiveness. In Chapter 2, I found that the gut microbiotas of non-human primates display predictable, host-species specific responses to captivity. In Chapter 3, I tested the hypothesis that cold-induced phenotypic plasticity is mediated by gut microbiota in captive tree swallow nestlings. Cold developmental temperatures induced plasticity in traits that prioritize thermoregulation, including a stronger glucocorticoid stress response, weaker negative feedback, increased pectoral muscle mass, and higher cold-induced metabolic rates. Antibiotic treatment reduced or eliminated thermal plasticity in each of these traits, suggesting that the ability to adapt plastically to thermal rearing environment may depend on host-associated microbiota. In Chapter 4, I investigated microbial dynamics in wild nestlings, experimentally lowering internal nest box temperature during early development and testing whether previously cold-exposed birds differed in their microbial or phenotypic response to a future cold snap. Cold-exposed birds reduced microbial diversity in response to a subsequent cold challenge. In Chapter 5, I co-developed a local elementary school outreach program on avian ecology. Due to COVID-19, we adapted our outreach program to deliver online by live-streaming nest boxes to the students’ virtual classroom. Collectively, the research components of my dissertation demonstrate that stressor-induced changes in gut microbiota may prime how hosts respond to and recover from future environmental stressors.