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Gas emissions from animal feeding operations (AFOs) degrade air quality and are threats to public health. Animal manure is a significant emission source, which is highly dependent on temperature and moisture content varying both spatially and temporally. We present design and operational features of an automated multiplexing system for chamber-based monitoring of greenhouse and regulated gas emissions from animal manure sources using a Fourier Transformed Infrared (FTIR) spectroscopy analyzer. The multiplexing system allows users to automate the chamber network, controlling the movement of chambers and accurately managing chamber air flow distribution. Chambers positioning was achieved with two 12-volt actuators with limit switches at the end of each cycle. Low-power latching solenoid valves were programmed to distribute air streams in concert with chamber placement. The sampled air stream was ultimately analyzed using an FTIR spectroscopy analyzer, which is capable of monitoring 15 pre-programmed gases simultaneously. System design, control circuit and system operating algorithms as well as data collection management are presented in this paper. The multiplexing system is anticipated to increase data collection efficiency and decrease the uncertainly associated with spatial variations in gas emission measurements from manure sources.