Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are ubiquitous and well-preserved sedimentary biomarkers. These compounds serve as important palaeoenvironmental indicators due to strong empirical correlations between brGDGT distributions and temperature and pH in modern environments. However, the mechanistic link between temperature, pH, and brGDGT production has been difficult to study due to uncertainty about the organisms and physiological conditions required for the synthesis of brGDGTs in nature. Here, we report that in the Acidobacterium Edaphobacter aggregans, severe oxygen limitation (1% O₂) leads to significant brGDGT production (2.9% of membrane lipids) with three structural varieties including an uncharacterised isomer of brGDGT Ic. Low O₂ as a physiological trigger for brGDGT production may help explain why brGDGT producers have been so difficult to identify, and provides a new path towards uncovering the genetic basis and biological function of brGDGTs. If the oxygen effects observed here apply more broadly, the empirical calibrations for brGDGT-based temperature and pH reconstructions may currently be missing the effects of oxygen as a relevant and possibly dominant control in the environmental distributions of brGDGTs.