By determining the source or sink strength of the three major agricultural greenhouse gases (GHG), nitrous oxide (N2O), methane (CH4) and carbon dioxide (CO2) in terms of their global warming potential (GWP), it becomes possible to directly evaluate options for GHG mitigation in agriculture. Situated at the Kellogg Biological Station (KBS) in SW Michigan, the Long-term Ecological Research (LTER) Program studies the ecology of intensive field crop ecosystems as part of a national network of sites. Also located at KBS, the Department of Energy (DOE) Great Lakes Bioenergy Research Center (GLBRC) has established a number of field–scale research sites to investigate the environmental sustainability of potential bioenergy cropping systems. These large–scale research programs require intensive, year-round static and automated gas sampling regimes to help fully elucidate the GHG footprint of the numerous treatments and management practices under investigation. Here we present an overview of the different GHG chamber types, sampling protocols, and analysis methodologies deployed at KBS. We highlight common concerns in relation to chamber methodology, and address the practical adaptations and testing carried out to ensure smooth day–to–day operations. More specifically, we address a new, streamlined data handling system that enables a robust, ‘hands-off’ approach to flux calculation, and an innovative Automated Trace Gas Trapping System geared to capturing long-term cumulative N2O emissions from a single deployment.