Jupiter, the fascinating largest planet in the solar system, has been visited by nine spacecraft, which have collected a significant amount of data about Jovian properties. In this paper, we show that one type of the in situ measurements on the relativistic electron fluxes could be used to probe dark matter (DM) and dark mediator between the dark sector and our visible world. Jupiter, with its immense weight and cool core, could be an ideal capturer for DM with masses around the GeV scale. The captured DM particles could annihilate into long-lived dark mediators such as dark photons, which subsequently decay into electrons and positrons outside Jupiter. The charged particles, trapped by the Jovian magnetic field, have been measured in Jupiter missions such as the Galileo probe and the Juno orbiter. We use the data available to set upper bounds on the cross section of DM scattering off nucleons, σχn, for dark mediators with lifetime of order $$ \mathcal{O} $$
O
(0.1–1) s. The results show that data from Jupiter missions already probe regions in the parameter space un- or under-explored by existing DM searches, e.g., constrain σχn of order (10−41–10−39) cm2 for 1 GeV DM dominantly annihilating into e+e− through dark mediators. This study serves as an example and an initial step to explore the full physics potential of the large planetary datasets from Jupiter missions. We also outline several other potential directions related to secondary products of electrons, positron signals and solar axions.