Summary: Tree stems from wetland, floodplain and upland forests can produce and emit methane (CH₄). Tree CH₄ stem emissions have high spatial and temporal variability, but there is no consensus on the biophysical mechanisms that drive stem CH₄ production and emissions. Here, we summarize up to 30 opportunities and challenges for stem CH₄ emissions research, which, when addressed, will improve estimates of the magnitudes, patterns and drivers of CH₄ emissions and trace their potential origin. We identified the need: (1) for both long‐term, high‐frequency measurements of stem CH₄ emissions to understand the fine‐scale processes, alongside rapid large‐scale measurements designed to understand the variability across individuals, species and ecosystems; (2) to identify microorganisms and biogeochemical pathways associated with CH₄ production; and (3) to develop a mechanistic model including passive and active transport of CH₄ from the soil–tree–atmosphere continuum. Addressing these challenges will help to constrain the magnitudes and patterns of CH₄ emissions, and allow for the integration of pathways and mechanisms of CH₄ production and emissions into process‐based models. These advances will facilitate the upscaling of stem CH₄ emissions to the ecosystem level and quantify the role of stem CH₄ emissions for the local to global CH₄ budget.