We present the first three-dimensional magnetohydrodynamic (MHD) simulations of the atmosphere of HD 209458b which self-consistently include reduction of winds due to the Lorentz force and Ohmic heating. We find overall wind structures similar to that seen in previous models of hot Jupiter atmospheres, with strong equatorial jets and meridional flows poleward near the day side and equatorward near the night side. Inclusion of magnetic fields slows those winds and leads to Ohmic dissipation. We find wind slowing ranging from 10%-40% for reasonable field strengths. We find Ohmic dissipation rates ~10^17 W at 100 bar, orders of magnitude too small to explain the inflated radius of this planet. Faster wind speeds, not achievable in these anelastic calculations, may be able to increase this value somewhat, but likely will not be able to close the gap necessary to explain the inflated radius. We demonstrate that the discrepancy between the simulations presented here and previous models is due to inadequate treatment of magnetic field geometry and evolution. Induced poloidal fields become much larger than those imposed, highlighting the need for a self-consistent MHD treatment of these hot atmospheres.