Summary Tree stems and soils can act as sources and sinks for the greenhouse gases (GHG) carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). Since both uptake and emission capacities can be large, especially in tropical rainforests, accurate assessments of the magnitudes and temporal variations of stem and soil GHG fluxes are required. We designed a new flexible stem chamber system for continuously measuring GHG fluxes in a French Guianese rainforest. Here, we describe this new system, which is connected to an automated soil GHG flux system, and discuss measurement uncertainty and potential error sources. In line with findings for soil GHG flux estimates, we demonstrated that lengthening the stem chamber closure time was required for accurate estimates of tree stem CH4 and N2O flux but not tree stem CO2 flux. The instrumented stem was a net source of CO2 and CH4 and a weak sink of N2O. Our experimental setup operated successfully in situ and provided continuous tree and soil GHG measurements at a high temporal resolution over an 11‐month period. This automated system is a major step forward in the measurement of GHG fluxes in stems and the atmosphere concurrently with soil GHG fluxes in tropical forest ecosystems.