Crassulacean acid metabolism (CAM) helps plants in arid regions to reduce water loss by opening their stomata and taking up carbon dioxide (CO2) during nighttime. While gas exchange in CAM plants has been mainly studied under controlled laboratory conditions, only a few ecosystem scale studies exist. Moreover, carbonyl sulfide (COS) has been used as a tracer for stomatal conductance, transpiration and photosynthesis in C3 and C4 plants, but no studies on CAM ecosystems have yet been published. Here we present the first ecosystem scale measurements of COS fluxes over Agave sisalana (CAM plant), commercially cultivated for its fiber. The measurements were made during the wet season in Kenya. The ecosystem was a consistent sink of COS, with higher uptake observed during nighttime (−11.5 pmol m−2 s−1) than during daytime (-5.6 pmol m−2 s−1). The magnitude of COS fluxes was comparable to non-growing season daytime fluxes reported for C3 and C4 plant dominated ecosystems. The soil was a small COS source (0.3 pmol m−2 s−1), with highest emissions under high radiation and temperature conditions. Using random forest modeling, we found that vapor pressure deficit, air temperature and soil water content were the most important drivers of nighttime ecosystem COS exchange (variable importance 0.25, 0.23 and 0.20, respectively), indicating the importance of stomatal limitation for COS fluxes. During daytime, air temperature, photosynthetically active radiation and soil temperature were the most important drivers (variable importances 0.19, 0.18 and 0.18, respectively). COS fluxes were further used to track canopy stomatal conductance and transpiration and compared to another transpiration estimate from the conditional eddy covariance method, which is based on raw water vapor and vertical wind data from eddy covariance. Conductance values ranged from 0.03 ± 0.06 mol m−2 s−1 during daytime to 0.06 ± 0.02 mol m−2 s−1 during nighttime. Transpiration was thus higher during nighttime than during daytime, reflecting the CAM gas exchange strategy.