Here we describe the results of an atomic resolution study of oxygen incorporation into bulk MgB2. We find that ∼20–100 nm sized precipitates are formed by ordered substitution of oxygen atoms onto boron lattice sites, while the basic bulk MgB2 crystal structure and orientation is preserved. The periodicity of the oxygen ordering is dictated by the oxygen concentration in the precipitates and primarily occurs in the (010) plane. The presence of these precipitates correlates well with an improved critical current density and superconducting transition behavior, implying that they act as pinning centers.