These data are associated with a study examining the effects of winter warming on the gut microbiome of the common wall lizard (Podarcis muralis). This work was supported by the Natural Environment Research Council (NERC) Envision Doctoral Training Programme (project number: 2737291) and an Amphibian and Reptile Conservation Trust grant awarded to M.R. The corresponding raw sequence data is available at European Nucleotide Archive (project accession number: PRJEB108057). Any queries or questions, please direct them to miaryras [at] gmail.com or k.macleod [at] bangor.ac.uk. Metadata is in Sheet 2 Content: Data used for the analysis of the gut microbiome diversity and composition of common wall lizard under different winter warming regimes. Manuscript abstract: Environmental temperature shapes ectotherm gut microbiomes through direct effects on community structure and indirect effects mediated by host physiology. Due to climate change, winter temperatures are rising, in some regions faster than summer temperatures. However, warming effects on the microbiome during overwintering remain poorly understood compared to the active season, limiting predictions of host-microbiome responses across the annual cycle. We experimentally tested how winter warming influences gut microbiome diversity and composition in the common wall lizard (Podarcis muralis). Thirty-nine lizards were overwintered under cold (4±1°C), mild (8±1°C), or fluctuating (5 days cold, 2 days mild) temperatures, and 80 faecal samples were collected post-emergence for 16S rRNA gene sequencing. Winter warming did not alter alpha diversity but induced consistent shifts in community composition relative to the cold treatment, with distinct responses to constant versus fluctuating warming. Constant mild temperatures enriched fewer taxa, including putatively opportunistic or pathogenic genera, potentially signalling microbiome imbalance. In contrast, fluctuating warming and the baseline cold treatment preserved a broader suite of fermentative bacteria, likely supporting more stable gut homeostasis. Both warming treatments increased directional dysbiosis relative to the cold treatment, though without increasing interindividual variability, indicating structured reassembly rather than stochastic change. Our findings suggest that winter warming can subtly negatively affect gut microbiomes and host health, while fluctuating temperatures may buffer negative effects. We show that overwintering is an important, yet overlooked, period through which climate warming can shape host-microbiome dynamics.