Jupiter’s atmosphere has a system of zones and belts punctuated by small and large vortices, the largest being the Great Red Spot. How these features change with depth is unknown, with theories of their structure ranging from shallow meteorological features to surface expressions of deep-seated convection. We present observations of atmospheric vortices using the Juno spacecraft’s Microwave Radiometer. We found vortex roots that extend deeper than the altitude at which water is expected to condense, and we identified density inversion layers. Our results constrain the three-dimensional structure of Jupiter’s vortices and their extension below the clouds.