The Fermi γ-ray telescope discovered a pair of bubbles at the Galactic center. These structures are spatially-correlated with the microwave emission detected by the WMAP and Planck satellites. These bubbles were likely inflated by a jet launched from the vicinity of a supermassive black hole in the Galactic center. Using MHD simulations, which self-consistently include interactions between cosmic rays and magnetic fields, we build models of the supersonic jet propagation, cosmic ray transport, and the magnetic field amplification within the Fermi bubbles. Our key findings are that: (1) the synthetic Fermi γ-ray and WMAP microwave spectra based on our simulations are consistent with the observations, suggesting that a single population of cosmic ray leptons may simultaneously explain the emission across a range of photon energies; (2) the model fits the observed centrally-peaked microwave emission if a second, more recent, pair of jets embedded in the Fermi bubbles is included in the model. This is consistent with the observationally-based suggestion made by Su & Finkbeiner (2012); (3) the radio emission from the bubbles is expected to be strongly polarized due to the relatively high level of field ordering caused by elongated turbulent vortices. This effect is caused by the interaction of the shocks driven by the jets with the preexisting interstellar medium turbulence; (4) a layer of enhanced rotation measure in the shock-compressed region could exist in the bubble vicinity but the level of this enhancement depends on the details of the magnetic topology.