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Water and ammonia vapors are known to be the major sources of spectral absorption at pressure levels observed by the microwave radiometer (MWR) on Juno. However, the brightness temperatures and limb darkening observed by the MWR at its longest-wavelength channel of 50 cm (600 MHz) in the first nine perijove passes indicate the existence of an additional source of opacity in the deep atmosphere of Jupiter (pressures beyond 100 bar). The absorption properties of ammonia and water vapor, and their relative abundances in Jupiter’s atmosphere, do not provide sufficient opacity in the deep atmosphere to explain the 600 MHz channel observation. Here we show that free electrons due to the ionization of alkali metals, i.e., sodium and potassium, with subsolar metallicity, [M/H] (log-based 10 relative concentration to solar) in the range of [M/H] = −2 to [M/H] = −5, can provide the missing source of opacity in the deep atmosphere. If the alkali metals are not the source of additional opacity in the MWR data, then their metallicity at 1000 bars can only be even lower. This upper bound of −2 on the metallicity of the alkali metals contrasts with the other heavy elements—C, N, S, Ar, Kr, and Xe—that are all enriched relative to their solar abundances, having a metallicity of approximately +0.5.