AbstractGreenhouse gas emissions from managed peatlands have not been extensively studied in Western Patagonia. The objective of this study was to assess the annual CO2 emission from microbial carbon (C) mineralization in a peatland site under not saturated conditions at Tierra del Fuego. The annual CO2 emissions were measured from unsaturated soil samples (n = 41) under soil incubation at seasonal local temperatures to simulate CO2 emissions for a year, using a non‐dispersive infrared gas analyser. Spatial models for total soil C and CO2 were calculated using discrete and continuous variables. The annual mean of measured cumulative CO2 was 1,358 µg CO2 g soil−1, lower than Northern peatlands, and 82% of the C mineralization occurred in the warmer season. The modelled CO2 in the warmer season showed levels of CO2 as high as 4 mg CO2 g soil−1, but 66% of the area showed between 600–2000 µg CO2 g soil−1, which is 28%–92% and 9%–32% of CO2 values reported for crop rotations. Consequently, after a potential habilitation of the study area for agricultural use, the soil CO2 emissions from heterotrophic activity would become a C source to the global CO2 emissions. This ecosystem is highly exposed to the effects of the land‐use change, and global temperature increase.