Atomic structures of single-crystalline iron-based nanowires crystallized inside multi-walled carbon nanotubes during pyrolysis on silicon substrates with ferrocene as a precursor were analyzed using high-resolution analytical transmission electron microscopy and electron diffraction. Standard crystal lattices, namely body-centered cubic (bcc) α-Fe, face-centered cubic (fcc) γ-Fe and orthorhombic cementite Fe₃C, were all found to form inside the nanotubes. A fraction of α-Fe nanowires, thermodynamically favorable at room temperature, was found to be dominant. Both bcc and fcc nanowires display a wide variety of lattice planes being parallel to the nanotube walls, with none of the orientations being preferable. The minor fraction of the nanowires had unidentified long-period crystal lattices with doubled or tripled periodicities as compared to those found in the standard cubic iron phases. The crystal matching of these unusual structures to stable orthorhombic Fe₃C or less stable iron carbides, e.g., Fe₅C₂, Fe₇C₃, failed. The non-conventional phases were tentatively assigned to rarely seen silicon-doped octahedral iron carbides. Both long-period and standard cementite nanowires exhibited well-defined transient zones in the vicinity of nanowire–tube shell interfaces, where perfectly ordered carbide lattice fringes disappeared. The results suggest the non-existence of metastable equilibrium in the nanoscale Fe–C system between carbide and graphite phases during iron crystallization inside graphitic tubular channels.