Tree stems from wetland, floodplain and upland forests can produce and emit methane (CH ₄ ). Tree CH ₄ stem emissions have high spatial and temporal variability, but there is no consensus on the biophysical mechanisms that drive stem CH ₄ production and emissions. Here, we summarize up to 30 opportunities and challenges for stem CH ₄ emissions research, which, when addressed, will improve estimates of the magnitudes, patterns and drivers of CH ₄ emissions and trace their potential origin. We identified the need: (1) for both long-term, high-frequency measurements of stem CH ₄ 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 CH ₄ production; and (3) to develop a mechanistic model including passive and active transport of CH ₄ from the soil–tree–atmosphere continuum. Addressing these challenges will help to constrain the magnitudes and patterns of CH ₄ emissions, and allow for the integration of pathways and mechanisms of CH ₄ production and emissions into process-based models. These advances will facilitate the upscaling of stem CH ₄ emissions to the ecosystem level and quantify the role of stem CH ₄ emissions for the local to global CH ₄ budget.