We present a surface x-ray diffraction study of the interface geometric structure in the Fe/MgO/Fe(001) magnetic tunnel junction (MTJ). While the lower MgO/Fe(001) interface is characterized by a substoichiometric FeO_x (x=0.6±0.1) layer in agreement with previous studies, growth of Fe on the MgO spacer and the upper Fe/MgO interface structure strongly depends on the preparation method. If 0.4 monolayers of Fe are initially deposited in ambient oxygen atmosphere (p=10⁻⁷ mbar) followed by Fe deposition under ultrahigh-vacuum (UHV) conditions, structural coherence across the trilayer junction is observed. In this case, substoichiometric FeO_x layers are present at both Fe/MgO interfaces corresponding to a symmetric MTJ structure. In contrast, lattice registry is not preserved if Fe deposition is carried out solely under UHV conditions. Our results might have important implications for the preparation of magnetic tunnel junctions optimized to achieve giant tunneling-magnetoresistance amplitudes.