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<p>Methane (CH<span class="inline-formula">₄</span>) emissions from wetlands are likely increasing and important in global climate change assessments. However, contemporary terrestrial biogeochemical model predictions of CH<span class="inline-formula">₄</span> emissions are very uncertain, at least in part due to prescribed temperature sensitivity of CH<span class="inline-formula">₄</span> production and emission. While statistically consistent apparent CH<span class="inline-formula">₄</span> emission temperature dependencies have been inferred from meta-analyses across microbial to ecosystem scales, year-round ecosystem-scale observations have contradicted that finding. Here, we show that apparent CH<span class="inline-formula">₄</span> emission temperature dependencies inferred from year-round chamber measurements exhibit substantial intra-seasonal variability, suggesting that using static temperature relations to predict CH<span class="inline-formula">₄</span> emissions is mechanistically flawed. Our model results indicate that such intra-seasonal variability is driven by substrate-mediated microbial and abiotic interactions: seasonal cycles in substrate availability favors CH<span class="inline-formula">₄</span> production later in the season, leading to hysteretic temperature sensitivity of CH<span class="inline-formula">₄</span> production and emission. Our findings demonstrate the uncertainty of inferring CH<span class="inline-formula">₄</span> emission or production rates from temperature alone and highlight the need to represent microbial and abiotic interactions in wetland biogeochemical models.</p>