Highly B‐site ordered Pb2ScTaO6 crystals are studied as a function of temperature via dielectric spectroscopy and in situ high‐dynamic‐range electron diffraction. The degree of ordering is examined on the local and macroscopic scale and is determined to be 76%. Novel analysis of the electron diffraction patterns provides structural information with two types of antiferroelectric displacements determined to be present in the polar structure. It is then found that a low‐temperature transition occurs on cooling at ≈210 K that is not present on heating. This phenomenon is discussed in terms of the freezing of dynamic polar nanodomains where a high density of domain walls creates a metastable state.