Jupiter’s upper atmosphere is composed of a neutral thermosphere and charged ionosphere. In the latter, the dominant molecular ion H3+ emits in the near-infrared, allowing for the remote exploration of the physical properties of the upper atmosphere. However, the Jovian low-latitude ionosphere remains largely unexplored because H3+ emissions from this region are faint and spectrally entangled with bright neutral species, such as CH4. Here, we present James Webb Space Telescope H3+ observations of Jupiter’s low-latitude ionosphere in the region of the Great Red Spot, showing unexpected small-scale intensity features such as arcs, bands and spots. Our observations may imply that the low-latitude ionosphere of Jupiter is strongly coupled to the lower atmosphere via gravity waves that superimpose to produce this complex and intricate morphology.