Microbial community metabolic balance (i.e., the ratio between photosynthesis and community respiration) is critical for assessing the strength of the biological carbon pump and its importance for the marine food web. This study aimed at characterizing the microbial community metabolic balance (hereinafter referred to as metabolic balance) in the Beagle Channel (BC, 54°S, 68° W), a sub-Antarctic environment that connects the Pacific and Atlantic Oceans at the southernmost extreme of South America. During a binational Chilean-Argentinian cruise along the eastern BC in the austral spring (November 2019), oxygen production and consumption rates were estimated in vitro after 12-h light and dark incubations. Phytoplankton primary productivity was additionally assessed using in vivo active fluorescence techniques. Environmental conditions (temperature, salinity, nutrients, dissolved oxygen, carbonate system and light) and the composition of the plankton community (i.e., phytoplankton and bacteria) were analyzed to assess the factors controlling productivity in the BC. Finally, we explored the role of the microbial community metabolic balance in modulating CO2 uptake by means of high-resolution underway CO2 fugacities (fCO2). Results showed a highly dynamic and rapidly changing system, with gross primary production (GPP) rates presenting a west-east gradient, with minimum values in the western portion of the study area (0.63 ± 0.12 mmol O2 m−3 d−1) and maximum values towards the Atlantic (13.87 ± 2.00 mmol O2 m−3 d−1). Community respiration rates were high (mean: 2.81 mmol O2 m−3 d−1) and positively correlated with GPP. Although net community production (NCP) was relatively low (0.25–3.27 mmol O2 m−3d−1), the P:R ratio suggests the prevalence of autotrophic communities, dominated by chain forming diatoms, mainly in the eastern portion (NCP: 3.27 mmol O2 m−3 d−1). Thermohaline conditions played a key role in regulating the productive capacity of the BC and in the sea-air CO2 exchange, except in the most productive stations, where biological production fueled fCO2 dynamics.