The Amazon rainforest is the world’s largest source of reactive volatile isoprenoids to the atmosphere. It is generally assumed that these emissions are products of photosynthetically driven secondary metabolism and released from the rainforest canopy from where they influence the oxidative capacity through reaction with hydroxyl radicals (OH) and ozone (O3). However, recent volatile organic compound (VOC) budgeting experiments (based on OH reactivity) show that further important sources remain to be discovered. Here we show that soil microorganisms are a strong, unaccounted source of highly reactive and previously unreported sesquiterpenes (C15H24; SQT). The emission rate and chemical speciation of soil SQTs were determined as a function of soil moisture, oxygen, and rRNA transcript abundance in the laboratory. Based on these results a model was developed to predict soil-atmosphere SQT fluxes. Simulated results compared closely with SQT flux measurements in the field, so a two-year period (2014-2015) was modelled based on in-situ rainfall and soil moisture measurements. It was found SQT emissions from a Terra Firme soil in the dry season were in comparable magnitude to current global model canopy emissions and dominated O3 reactivity on the forest floor, establishing an important ecological connection between soil microbes and atmospherically relevant SQTs.