<p>Tropical peatlands are carbon-dense ecosystems that are significant sources of atmospheric methane (CH₄). Recent work has demonstrated the importance of trees as an emission pathway for CH₄ from the peat to the atmosphere. However, there remain questions over the processes of CH₄ production in these systems and how they relate to substrate supply. Principally, these questions relate to the relative contribution of recent photosynthetically fixed carbon, released as root exudates, versus carbon substrate supply from the slowly decomposing peat matrix to CH₄ emissions within these ecosystems. Here, we examined the role of root inputs in regulating CH₄ production inferred from soil emissions using a combination of in situ tree girdling, in situ¹³C natural abundance labelling via stem injections, and a ¹³CO₂ labelling of transplanted plants of two contrasting plant functional types, a broadleaved evergreen tree, and a canopy palm. Girdling of broadleaved evergreen trees reduced CH₄ fluxes by up to 67%. Stem injections of trees and palms with a natural abundance label resulted in significant isotopic enrichment of CH₄ fluxes, reinforcing the link between root carbon inputs and peat CH₄ fluxes. <i>Ex situ</i>¹³CO₂ labelling of plants resulted in significant ¹³C enrichment of peat CH₄ fluxes. Taken together, our results demonstrate for the first time that plant root exudates make a substantial contribution to CH₄ production in tropical peatlands.</p>