Over the last decades and due to the current climate change situation, the study of the impacts of human activities on climate has reached great importance, with agriculture being one of the main sources of soil greenhouse gas. There are different techniques to quantify the soil gas fluxes, such as micrometeorological techniques or chamber techniques, with the last one being capable of assessing different treatments at the same site. Manual chambers are the most common technique. However, manual chambers are characterized by low sampling frequency; typically, one sample per day is considered to be a high sampling frequency. Therefore, a great deal of effort is required to monitor short-term emission events such as fertilization or rewetting. For this reason, automated chamber systems present an opportunity to improve soil gas flux determination, but their distribution is still scarce due to the cost and challenging technical implementation. The objective of this study was to develop an automated chamber system for agricultural systems and to compare it with a manual chamber system. Moreover, over a period of 1 month, the soil gas fluxes were determined by both systems to compare their capabilities in capturing the temporal variability of soil gas emissions. The automated system reported soil greenhouse gas (GHG) fluxes that were up to 58 % and 40 % greater for CO2 and N2O fluxes compared to the manual chamber system. Additionally, the higher sampling frequency of the automated chamber system allowed us to capture the daily flux variations, resulting in a more accurate estimation of cumulative soil gas emissions. Furthermore, the assessment of various sampling intervals for single-day measurements indicated that between 10:00 and 12:00 LT was the optimal time interval for soil gas sampling in order to obtain representative daily emissions. This study emphasizes the importance of chamber dimension and shape in the development of chamber systems, as well as the sampling frequency and sampling hour for manual chamber systems.