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The fluxes of different greenhouse gas (GHG) species have long been studied using a variety of techniques, with the choice of method largely determined by the measurement scale. Small-scale fluxes such as soil chamber measurements may be made using closed transient approaches, whereas direct micrometeorological measurement of ecosystem-scale fluxes predominantly employs eddy covariance or related methodologies. However, methods to directly quantify plant-mediated fluxes at the leaf scale remain limited. Increasingly, plant-mediated transport (PMT) and plant-mediated exchange (PME) are recognised as important, and in some ecosystems even dominant pathways by which some soil-produced GHGs reach the atmosphere. These processes are influenced by both biotic and abiotic factors, and physiological characteristics of the plant, such as stomatal conductance, are thought to play a significant role. However, a limited body of literature constrains our understanding of this component of GHG flux, largely due to the lack of appropriate instrumentation and methodologies to quantify these fluxes. Clipping studies have been used to remove vegetation from plots and monitor net changes in flux, but this precludes investigation of interactions between plant physiology and the GHG flux. Plant physiological responses are typically measured in an open flow through system to minimise perturbation of physiology. Portable photosynthesis systems measure CO2 and H2O concentrations before and after interacting with the leaf. The differences between these concentrations (ΔCO2, ΔH2O) permit calculation of physiological parameters including net CO2 assimilation (A), intercellular CO2 concentration (Ci), and stomatal conductance to water vapour (gsw) while the chamber is continuously refreshed with stable air, allowing the maintenance of the leaf in a steady physiological state. However, the open flow-through nature of the photosynthesis system has traditionally made quantification of plant-mediated trace gas fluxes, such as CH4 and N2O, challenging. The surface area of plant material enclosed is typically small, and the relatively small changes in trace gas concentrations require a high degree of precision to resolve. Additional complexity arises from the large differences in H2O concentration before and after interaction with the leaf due to transpiration. Most systems also show a sensitivity to changing CO2 concentration, which is commonly utilised in plant physiology measurements. Here we describe and characterise a system that integrates trace gas measurements with a commercial photosynthesis system (LI-COR LI-6800), managing water transients and integrating data from the various gas analysers, including real-time on-board flux calculations. Presented are two commercial OF-CEAS trace gas analysers, measuring CH4 and N2O (LI-COR LI-7810 and LI-7820 respectively). We examine the impact of averaging interval on measurement precision for a range of CO2 mole fractions and assess the dependence of trace gas mole fraction to changing CO2 mole fractions. We also present a sensitivity analysis for zero trace gas flux.