Three-dimensional elemental distributions in magnetic tunnel junctions containing naturally oxidized MgO tunnel barriers are characterized using atom-probe tomography. Replacing the CoFeB free layer (reference layer) with a CoFe/CoFeB (CoFeB/CoFe) bilayer increases the magnetoresistance from 105% to 192% and decreases the resistance-area product from 14.5 to 3.4 Ω μm2. The CoFe/CoFeB bilayer improves the compositional uniformity within the free layer by nucleating CoFeB crystals across the entire layer, resulting in a homogeneous barrier/free layer interface. In contrast, the simple CoFeB free layer partially crystallizes with composition differences from grain to grain (5–30 nm), degrading the tunnel junction performance.