We investigate auroral energy deposition by using a nonhydrostatic global atmospheric model coupled to a two‐stream electron transport model. We present several electron beam study cases, discussing energy flux and electron energy effects on the ion and neutral densities, the atmospheric thermal profile, H3+ and hydrocarbon infrared (IR) emissions, H2 far ultraviolet (FUV) emissions and color ratios, and vibrationally excited molecular hydrogen. Using the nonhydrostatic Jupiter Global Ionosphere‐Thermosphere Model, we find that FUV spectral characteristics consistent with previous Hubble Space Telescope results derive primarily from electrons with energies above 10 keV, over energy fluxes of 10–100 erg/cm2 s, while IR emissions are predominantly due to electrons with energies below 10 keV, over energy fluxes of 10–100 erg/cm2 s. Electrons with energies below about 10 keV produce enough H2(ν) to deplete the H+ population, modifying the ionospheric composition, and consequently the H3+ emissions, which can be used to directly relate H2 vibrational excitation to auroral observations. New observations by Juno will provide better electron energy distributions to constrain the electron energy spectrum and magnitude at the upper boundary of the model and simultaneously provide a determination of the FUV and IR spectra that can be cross‐correlated with the observations.